diff --git a/CHANGELOG.md b/CHANGELOG.md index 7c459f3..9451ef6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,17 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] +## [1.3.0] - 2018-11-13 +### Added +- Support for one more alternative assembler: wtdbg2. +### Changed +- Substantially more automated installation/setup process. +- Software version or downloading URL updates for a number of dependencies. +### Fixed +- Bugs introduced due to changes made for file/parameter names in the LRSDAY.01.Long-read-based_Genome_Assembly.sh script when using some alternative assemblers. +- Mismatched step numbers and file names in the manual due to previous version changes. +- Typos in the manual. + ## [1.2.0] - 2018-10-15 ### Added - Support for adapter trimming for Nanopore reads (via Porechop). diff --git a/Example_Outputs/SK1.assembly.final.fa.gz b/Example_Outputs/SK1.assembly.final.fa.gz index e0a8f2a..5d041e7 100644 Binary files a/Example_Outputs/SK1.assembly.final.fa.gz and b/Example_Outputs/SK1.assembly.final.fa.gz differ diff --git a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz index 02d4569..07d08ac 100644 Binary files a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz and b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz differ diff --git a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz index 0bbb1cf..3854c43 100644 Binary files a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz and b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz differ diff --git a/Example_Outputs/SK1.assembly.final.filter.pdf b/Example_Outputs/SK1.assembly.final.filter.pdf index 7e81d57..0aa8e40 100644 Binary files a/Example_Outputs/SK1.assembly.final.filter.pdf and b/Example_Outputs/SK1.assembly.final.filter.pdf differ diff --git a/Example_Outputs/SK1.assembly.final.stats.txt b/Example_Outputs/SK1.assembly.final.stats.txt index 9f82176..4a1376c 100644 --- a/Example_Outputs/SK1.assembly.final.stats.txt +++ b/Example_Outputs/SK1.assembly.final.stats.txt @@ -1,17 +1,17 @@ -total sequence count: 33 -total sequence length: 12490496 +total sequence count: 34 +total sequence length: 12448004 min sequence length: 1248 -max sequence length: 1480288 -mean sequence length: 378499.88 -median sequence length: 84643.00 -N50: 923711 +max sequence length: 1480301 +mean sequence length: 366117.76 +median sequence length: 60826.50 +N50: 923676 L50: 6 -N90: 341493 +N90: 341518 L90: 14 -A%: 30.88 -T%: 30.79 -G%: 19.13 -C%: 19.16 -AT%: 61.67 -GC%: 38.29 +A%: 30.89 +T%: 30.81 +G%: 19.14 +C%: 19.13 +AT%: 61.70 +GC%: 38.26 N%: 0.04 diff --git a/Example_Outputs/SK1.final.cds.fa.gz b/Example_Outputs/SK1.final.cds.fa.gz index a682a86..fcd514d 100644 Binary files a/Example_Outputs/SK1.final.cds.fa.gz and b/Example_Outputs/SK1.final.cds.fa.gz differ diff --git a/Example_Outputs/SK1.final.gff3.gz b/Example_Outputs/SK1.final.gff3.gz index 76df663..39247da 100644 Binary files a/Example_Outputs/SK1.final.gff3.gz and b/Example_Outputs/SK1.final.gff3.gz differ diff --git a/Example_Outputs/SK1.final.manual_check.list b/Example_Outputs/SK1.final.manual_check.list index c4c707d..b54d801 100644 --- a/Example_Outputs/SK1.final.manual_check.list +++ b/Example_Outputs/SK1.final.manual_check.list @@ -1,245 +1,244 @@ -SK1_G0000060|SK1_G0000060.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0000720|SK1_G0000720.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0000820|SK1_G0000820.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0001040|SK1_G0001040.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0001150|SK1_G0001150.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0001200|SK1_G0001200.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0001400|SK1_G0001400.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0001580|SK1_G0001580.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0001820|SK1_G0001820.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0002610|SK1_G0002610.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0002800|SK1_G0002800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0000050|SK1_G0000050.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0000710|SK1_G0000710.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0000810|SK1_G0000810.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0000950|SK1_G0000950.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0000970|SK1_G0000970.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0001060|SK1_G0001060.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0001170|SK1_G0001170.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0001220|SK1_G0001220.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0001420|SK1_G0001420.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0001600|SK1_G0001600.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0001750|SK1_G0001750.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0001850|SK1_G0001850.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0002640|SK1_G0002640.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0002830|SK1_G0002830.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0002890|SK1_G0002890.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0003740|SK1_G0003740.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0004120|SK1_G0004120.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0004460|SK1_G0004460.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0004870|SK1_G0004870.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0005410|SK1_G0005410.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0005490|SK1_G0005490.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0005570|SK1_G0005570.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0005770|SK1_G0005770.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0002860|SK1_G0002860.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0002920|SK1_G0002920.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0003770|SK1_G0003770.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0004150|SK1_G0004150.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0004490|SK1_G0004490.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0004900|SK1_G0004900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0005440|SK1_G0005440.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0005520|SK1_G0005520.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0005600|SK1_G0005600.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0005800|SK1_G0005800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0005810|SK1_G0005810.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0005830|SK1_G0005830.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0005900|SK1_G0005900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0005980|SK1_G0005980.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0006400|SK1_G0006400.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0006450|SK1_G0006450.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 -SK1_G0006460|SK1_G0006460.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1 -SK1_G0006600|SK1_G0006600.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0007680|SK1_G0007680.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0007770|SK1_G0007770.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0008070|SK1_G0008070.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0008100|SK1_G0008100.mRNA.1 incorrect CDS length -SK1_G0008110|SK1_G0008110.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0008120|SK1_G0008120.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0009310|SK1_G0009310.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0009970|SK1_G0009970.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0010050|SK1_G0010050.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0010340|SK1_G0010340.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0011090|SK1_G0011090.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0011580|SK1_G0011580.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0012330|SK1_G0012330.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0012480|SK1_G0012480.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0012690|SK1_G0012690.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0012700|SK1_G0012700.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0012880|SK1_G0012880.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0013360|SK1_G0013360.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0013380|SK1_G0013380.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0013670|SK1_G0013670.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 -SK1_G0013710|SK1_G0013710.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0013720|SK1_G0013720.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0013790|SK1_G0013790.mRNA.1 incorrect CDS length -SK1_G0013820|SK1_G0013820.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0014540|SK1_G0014540.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0014590|SK1_G0014590.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0014990|SK1_G0014990.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0015130|SK1_G0015130.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0015520|SK1_G0015520.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0005840|SK1_G0005840.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0005860|SK1_G0005860.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0005930|SK1_G0005930.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0006010|SK1_G0006010.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0006430|SK1_G0006430.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0006480|SK1_G0006480.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 +SK1_G0006490|SK1_G0006490.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1 +SK1_G0006630|SK1_G0006630.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0007710|SK1_G0007710.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0007800|SK1_G0007800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0008100|SK1_G0008100.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0008130|SK1_G0008130.mRNA.1 incorrect CDS length +SK1_G0008140|SK1_G0008140.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0008150|SK1_G0008150.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0009340|SK1_G0009340.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0010000|SK1_G0010000.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0010080|SK1_G0010080.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0010370|SK1_G0010370.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0011120|SK1_G0011120.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0011610|SK1_G0011610.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0012360|SK1_G0012360.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0012510|SK1_G0012510.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0012720|SK1_G0012720.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0012730|SK1_G0012730.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0012910|SK1_G0012910.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0013390|SK1_G0013390.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0013410|SK1_G0013410.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0013710|SK1_G0013710.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 +SK1_G0013750|SK1_G0013750.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0013760|SK1_G0013760.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0013810|SK1_G0013810.mRNA.1 incorrect CDS length +SK1_G0013820|SK1_G0013820.mRNA.1 incorrect CDS length +SK1_G0013830|SK1_G0013830.mRNA.1 incorrect CDS length +SK1_G0013850|SK1_G0013850.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0014570|SK1_G0014570.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0014620|SK1_G0014620.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0015020|SK1_G0015020.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0015160|SK1_G0015160.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0015550|SK1_G0015550.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0016470|SK1_G0016470.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0016600|SK1_G0016600.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0016820|SK1_G0016820.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0016830|SK1_G0016830.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0016930|SK1_G0016930.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0016940|SK1_G0016940.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0017410|SK1_G0017410.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0017490|SK1_G0017490.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0017750|SK1_G0017750.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0017760|SK1_G0017760.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0017770|SK1_G0017770.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0017920|SK1_G0017920.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0018150|SK1_G0018150.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0018530|SK1_G0018530.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0019080|SK1_G0019080.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0019370|SK1_G0019370.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0019480|SK1_G0019480.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0020130|SK1_G0020130.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0021540|SK1_G0021540.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0021780|SK1_G0021780.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0022750|SK1_G0022750.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0022790|SK1_G0022790.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0022820|SK1_G0022820.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0022900|SK1_G0022900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0022930|SK1_G0022930.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0023540|SK1_G0023540.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0023590|SK1_G0023590.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0023780|SK1_G0023780.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0015580|SK1_G0015580.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0016490|SK1_G0016490.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1 +SK1_G0016520|SK1_G0016520.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0016650|SK1_G0016650.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0016870|SK1_G0016870.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0016880|SK1_G0016880.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0016980|SK1_G0016980.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0016990|SK1_G0016990.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0017460|SK1_G0017460.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0017540|SK1_G0017540.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0017800|SK1_G0017800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0017810|SK1_G0017810.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0017820|SK1_G0017820.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0017970|SK1_G0017970.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0018200|SK1_G0018200.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0018580|SK1_G0018580.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0019130|SK1_G0019130.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0019420|SK1_G0019420.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0019530|SK1_G0019530.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0020180|SK1_G0020180.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0021590|SK1_G0021590.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0021830|SK1_G0021830.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0022800|SK1_G0022800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0022840|SK1_G0022840.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0022870|SK1_G0022870.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0022920|SK1_G0022920.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0022950|SK1_G0022950.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0023560|SK1_G0023560.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0023610|SK1_G0023610.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0023800|SK1_G0023800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0023860|SK1_G0023860.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0024160|SK1_G0024160.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0024190|SK1_G0024190.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0024370|SK1_G0024370.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0024410|SK1_G0024410.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0024800|SK1_G0024800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0025240|SK1_G0025240.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0025380|SK1_G0025380.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0025420|SK1_G0025420.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0025580|SK1_G0025580.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0023820|SK1_G0023820.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0023880|SK1_G0023880.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0024180|SK1_G0024180.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0024210|SK1_G0024210.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0024390|SK1_G0024390.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0024430|SK1_G0024430.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0024820|SK1_G0024820.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0025260|SK1_G0025260.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0025400|SK1_G0025400.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0025440|SK1_G0025440.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0025600|SK1_G0025600.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0025860|SK1_G0025860.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 -SK1_G0025950|SK1_G0025950.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0026240|SK1_G0026240.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0026390|SK1_G0026390.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0026480|SK1_G0026480.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0026520|SK1_G0026520.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0026670|SK1_G0026670.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0026870|SK1_G0026870.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0026900|SK1_G0026900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0027170|SK1_G0027170.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0027620|SK1_G0027620.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0027670|SK1_G0027670.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 -SK1_G0027700|SK1_G0027700.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 -SK1_G0027710|SK1_G0027710.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0025620|SK1_G0025620.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0025880|SK1_G0025880.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 +SK1_G0025970|SK1_G0025970.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0026260|SK1_G0026260.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0026410|SK1_G0026410.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0026500|SK1_G0026500.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0026540|SK1_G0026540.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0026690|SK1_G0026690.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0026890|SK1_G0026890.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0026920|SK1_G0026920.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0027190|SK1_G0027190.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0027640|SK1_G0027640.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0027710|SK1_G0027710.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 +SK1_G0027720|SK1_G0027720.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0027730|SK1_G0027730.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0027760|SK1_G0027760.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0027910|SK1_G0027910.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0028500|SK1_G0028500.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0029450|SK1_G0029450.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0029520|SK1_G0029520.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0029880|SK1_G0029880.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0030010|SK1_G0030010.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0031020|SK1_G0031020.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0031060|SK1_G0031060.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0031120|SK1_G0031120.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0031180|SK1_G0031180.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 -SK1_G0031190|SK1_G0031190.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0031800|SK1_G0031800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0032210|SK1_G0032210.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0032370|SK1_G0032370.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0033280|SK1_G0033280.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0033380|SK1_G0033380.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0033390|SK1_G0033390.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0034220|SK1_G0034220.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0034370|SK1_G0034370.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0034880|SK1_G0034880.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0035480|SK1_G0035480.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0035700|SK1_G0035700.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0035850|SK1_G0035850.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0036760|SK1_G0036760.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0036870|SK1_G0036870.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0037750|SK1_G0037750.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0038570|SK1_G0038570.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0038660|SK1_G0038660.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0039110|SK1_G0039110.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0039190|SK1_G0039190.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0039290|SK1_G0039290.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0039310|SK1_G0039310.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0039620|SK1_G0039620.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0039660|SK1_G0039660.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0039770|SK1_G0039770.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0039830|SK1_G0039830.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0039950|SK1_G0039950.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0040210|SK1_G0040210.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0040220|SK1_G0040220.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0040520|SK1_G0040520.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0041530|SK1_G0041530.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0041760|SK1_G0041760.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0041970|SK1_G0041970.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0042280|SK1_G0042280.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0042350|SK1_G0042350.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0042590|SK1_G0042590.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0043670|SK1_G0043670.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0043700|SK1_G0043700.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0043720|SK1_G0043720.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0044020|SK1_G0044020.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0044030|SK1_G0044030.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0044300|SK1_G0044300.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0044350|SK1_G0044350.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0044940|SK1_G0044940.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0045120|SK1_G0045120.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0045490|SK1_G0045490.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1 -SK1_G0045580|SK1_G0045580.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0045870|SK1_G0045870.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0046120|SK1_G0046120.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0046280|SK1_G0046280.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0047260|SK1_G0047260.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0047270|SK1_G0047270.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0047350|SK1_G0047350.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0027750|SK1_G0027750.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0027780|SK1_G0027780.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0027930|SK1_G0027930.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0028520|SK1_G0028520.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0029470|SK1_G0029470.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0029540|SK1_G0029540.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0029900|SK1_G0029900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0030030|SK1_G0030030.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0031040|SK1_G0031040.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0031080|SK1_G0031080.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0031140|SK1_G0031140.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0031200|SK1_G0031200.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 +SK1_G0031210|SK1_G0031210.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0031820|SK1_G0031820.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0032230|SK1_G0032230.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0032390|SK1_G0032390.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0033300|SK1_G0033300.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0033400|SK1_G0033400.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0033410|SK1_G0033410.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0034240|SK1_G0034240.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0034390|SK1_G0034390.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0034900|SK1_G0034900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0035500|SK1_G0035500.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0035720|SK1_G0035720.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0035870|SK1_G0035870.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0036790|SK1_G0036790.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0036900|SK1_G0036900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0037780|SK1_G0037780.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0038600|SK1_G0038600.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0038690|SK1_G0038690.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0039140|SK1_G0039140.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0039220|SK1_G0039220.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0039320|SK1_G0039320.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0039340|SK1_G0039340.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0039650|SK1_G0039650.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0039690|SK1_G0039690.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0039800|SK1_G0039800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0039860|SK1_G0039860.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0039980|SK1_G0039980.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0040240|SK1_G0040240.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0040250|SK1_G0040250.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0040550|SK1_G0040550.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0041560|SK1_G0041560.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0041790|SK1_G0041790.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0042000|SK1_G0042000.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0042310|SK1_G0042310.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0042380|SK1_G0042380.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0042620|SK1_G0042620.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0043700|SK1_G0043700.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0043730|SK1_G0043730.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0043750|SK1_G0043750.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0044050|SK1_G0044050.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0044060|SK1_G0044060.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0044330|SK1_G0044330.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0044380|SK1_G0044380.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0044970|SK1_G0044970.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0045150|SK1_G0045150.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0045520|SK1_G0045520.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1 +SK1_G0045610|SK1_G0045610.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0045900|SK1_G0045900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0046150|SK1_G0046150.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0046310|SK1_G0046310.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0047290|SK1_G0047290.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0047300|SK1_G0047300.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0047380|SK1_G0047380.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0047490|SK1_G0047490.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0047890|SK1_G0047890.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0047900|SK1_G0047900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0048590|SK1_G0048590.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0048600|SK1_G0048600.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0049260|SK1_G0049260.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0050140|SK1_G0050140.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0050990|SK1_G0050990.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0051150|SK1_G0051150.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0051220|SK1_G0051220.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0051550|SK1_G0051550.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0052250|SK1_G0052250.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0052490|SK1_G0052490.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0052500|SK1_G0052500.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0052640|SK1_G0052640.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0052670|SK1_G0052670.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length -SK1_G0052680|SK1_G0052680.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0052720|SK1_G0052720.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0053020|SK1_G0053020.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0053110|SK1_G0053110.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0053640|SK1_G0053640.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0053820|SK1_G0053820.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0054260|SK1_G0054260.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0054360|SK1_G0054360.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0054550|SK1_G0054550.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0055090|SK1_G0055090.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0055150|SK1_G0055150.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0055230|SK1_G0055230.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0055490|SK1_G0055490.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0055960|SK1_G0055960.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0056260|SK1_G0056260.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057380|SK1_G0057380.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057400|SK1_G0057400.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0047410|SK1_G0047410.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0047520|SK1_G0047520.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0047920|SK1_G0047920.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0047930|SK1_G0047930.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0048620|SK1_G0048620.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0048630|SK1_G0048630.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0049290|SK1_G0049290.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0050170|SK1_G0050170.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0051020|SK1_G0051020.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0051180|SK1_G0051180.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0051250|SK1_G0051250.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0051580|SK1_G0051580.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0052280|SK1_G0052280.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0052520|SK1_G0052520.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0052530|SK1_G0052530.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0052670|SK1_G0052670.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0052700|SK1_G0052700.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0052710|SK1_G0052710.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0052750|SK1_G0052750.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0053050|SK1_G0053050.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0053140|SK1_G0053140.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0053670|SK1_G0053670.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0053850|SK1_G0053850.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0054290|SK1_G0054290.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0054390|SK1_G0054390.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0054580|SK1_G0054580.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0055120|SK1_G0055120.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0055180|SK1_G0055180.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0055260|SK1_G0055260.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0055520|SK1_G0055520.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0055990|SK1_G0055990.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0056290|SK1_G0056290.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0057300|SK1_G0057300.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0057390|SK1_G0057390.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0057410|SK1_G0057410.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057420|SK1_G0057420.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057450|SK1_G0057450.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057650|SK1_G0057650.mRNA.1 incorrect CDS length -SK1_G0057710|SK1_G0057710.mRNA.1 incorrect CDS length -SK1_G0057750|SK1_G0057750.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 -SK1_G0057800|SK1_G0057800.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057830|SK1_G0057830.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057840|SK1_G0057840.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057870|SK1_G0057870.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057900|SK1_G0057900.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057930|SK1_G0057930.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0057460|SK1_G0057460.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0057480|SK1_G0057480.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0057500|SK1_G0057500.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0057510|SK1_G0057510.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0057570|SK1_G0057570.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0057590|SK1_G0057590.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0057750|SK1_G0057750.mRNA.1 incorrect CDS length +SK1_G0057780|SK1_G0057780.mRNA.1 incorrect CDS length +SK1_G0057800|SK1_G0057800.mRNA.1 incorrect CDS length +SK1_G0057960|SK1_G0057960.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0057970|SK1_G0057970.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0057990|SK1_G0057990.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0058000|SK1_G0058000.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0057980|SK1_G0057980.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0058010|SK1_G0058010.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0058110|SK1_G0058110.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0058120|SK1_G0058120.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0058160|SK1_G0058160.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0058240|SK1_G0058240.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0058020|SK1_G0058020.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0058030|SK1_G0058030.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0058070|SK1_G0058070.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) +SK1_G0058160|SK1_G0058160.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length +SK1_G0058260|SK1_G0058260.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) SK1_G0058280|SK1_G0058280.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0058430|SK1_G0058430.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0058470|SK1_G0058470.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0058530|SK1_G0058530.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s) -SK1_G0058570|SK1_G0058570.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 1 -SK1_G0058580|SK1_G0058580.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 1 cox2|cox2.mRNA.1 unexpected stop codon based on standard genentic code;your selected code table is 3;incorrect CDS length orf474|orf474.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 3;incorrect CDS length orf90|orf90.mRNA.1 unexpected start codon based on standard genentic code;your selected code table is 3 orf241|orf241.mRNA.1 unexpected start & end codons based on standard genentic code;your selected code table is 3;incorrect CDS length orf152|orf152.mRNA.1 incorrect CDS length -cox1|cox1.mRNA.1 incorrect CDS length diff --git a/Example_Outputs/SK1.final.pep.fa.gz b/Example_Outputs/SK1.final.pep.fa.gz index 7b173e2..97bae49 100644 Binary files a/Example_Outputs/SK1.final.pep.fa.gz and b/Example_Outputs/SK1.final.pep.fa.gz differ diff --git a/Example_Outputs/SK1.final.trimmed_cds.fa.gz b/Example_Outputs/SK1.final.trimmed_cds.fa.gz index 162e9de..b3a7aae 100644 Binary files a/Example_Outputs/SK1.final.trimmed_cds.fa.gz and b/Example_Outputs/SK1.final.trimmed_cds.fa.gz differ diff --git a/LRSDAY_flowchart.png b/LRSDAY_flowchart.png index 205c62b..8359bea 100644 Binary files a/LRSDAY_flowchart.png and b/LRSDAY_flowchart.png differ diff --git a/Manual.pdf b/Manual.pdf index 5d5808d..33fed57 100644 Binary files a/Manual.pdf and b/Manual.pdf differ diff --git a/Project_Template/01.Long-read-based_Genome_Assembly/LRSDAY.01.Long-read-based_Genome_Assembly.sh b/Project_Template/01.Long-read-based_Genome_Assembly/LRSDAY.01.Long-read-based_Genome_Assembly.sh index 16f7956..222af03 100755 --- a/Project_Template/01.Long-read-based_Genome_Assembly/LRSDAY.01.Long-read-based_Genome_Assembly.sh +++ b/Project_Template/01.Long-read-based_Genome_Assembly/LRSDAY.01.Long-read-based_Genome_Assembly.sh @@ -11,8 +11,8 @@ prefix="SK1" # The file name prefix for the output files. long_reads="./../00.Long_Reads/SK1.filtered_subreads.fastq.gz" # The file path of the long reads file (in fastq or fastq.gz format). long_reads_type="pacbio-raw" # The long reads data type. Use "pacbio-raw" or "pacbio-corrected" or "nanopore-raw" or "nanopore-corrected". Default = "pacbio-raw" for the testing example genome_size="12.5m" # The estimated genome size with the format of [g|m|k], e.g. 12.5m for 12.5 Mb. Default = "12.5m". -assembler="canu" # The long-read assembler: Use "canu" or "flye" or "smartdenovo" or "canu-flye" or "canu-smartdenovo". For "canu-flye" and "canu-smartdenovo", the assembler canu is used first to generate error-corrected reads from the raw reads and then the assembler flye/smartdenovo is used to assemble the genome. Based on our test, assembler="canu" generally gives the best result but will take substantially longer time than the other options. -customized_canu_parameters="-correctedErrorRate=0.04" # For assembler="canu" only. Users can set customized Canu assembly parameters here or simply leave it empty like "" to use Canu's default assembly parameter. For example you could set "-correctedErrorRate=0.04" for high coverage (>60X) PacBio data and "-correctedErrorRate=0.12 -overlapper=mhap -utgReAlign=true" for high coverage (>60X) Nanopore data to improve the assembly speed. More than one customized parameters can be set here as long as they are separeted by space (e.g. "-option1=XXX -option2=YYY -option3=ZZZ"). Please consult Canu's manual "http://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak" for advanced customization settings. Default = "-correctedErrorRate=0.04" for the testing example. +assembler="canu" # The long-read assembler: Use "canu" or "flye" or "wtdbg2" or "smartdenovo" or "canu-flye" or "canu-wtdbg2" or "canu-smartdenovo". For "canu-flye", "canu-wtdbg2", and "canu-smartdenovo", the assembler canu is used first to generate error-corrected reads from the raw reads and then the assembler flye/wtdbg2/smartdenovo is used to assemble the genome. Based on our test, assembler="canu" generally gives the best result but will take substantially longer time than the other options. +customized_canu_parameters="-correctedErrorRate=0.04" # For assembler="canu" only. Users can set customized Canu assembly parameters here or simply leave it empty like "" to use Canu's default assembly parameter. For example you could set "-correctedErrorRate=0.04" for high coverage (>60X) PacBio data and "-overlapper=mhap -utgReAlign=true" for high coverage (>60X) Nanopore data to improve the assembly speed. More than one customized parameters can be set here as long as they are separeted by space (e.g. "-option1=XXX -option2=YYY -option3=ZZZ"). Please consult Canu's manual "http://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak" for advanced customization settings. Default = "-correctedErrorRate=0.04" for the testing example. threads=1 # The number of threads to use. Default = 1. vcf="yes" # Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Otherwise use "no". Default = "yes". dotplot="yes" # Use "yes" if prefer to plot genome-wide dotplot based on the comparison with the reference genome below. Otherwise use "no". Default = "yes". @@ -59,25 +59,33 @@ then -${long_reads_type} $long_reads \ $customized_canu_parameters - perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i ./$out_dir/$prefix.contigs.fasta -o $prefix.assembly.$assembler.fa + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/$prefix.contigs.fasta -o $prefix.assembly.$assembler.fa elif [[ "$assembler" == "flye" ]] then if [[ "$long_reads_type" == "pacbio-corrected" ]] then - reads_type="pacbio-corr" + long_reads_type="pacbio-corr" elif [[ "$long_reads_type" == "nanopore-raw" ]] then - reads_type="nano-raw" + long_reads_type="nano-raw" elif [[ "$long_reads_type" == "nanopore-corrected" ]] then - reads_type="nano-corr" + long_reads_type="nano-corr" fi - $flye_new_dir/flye -o $out_dir \ + $flye_dir/flye -o $out_dir \ -t $threads \ -g $genome_size \ --${long_reads_type} $long_reads \ -i 2 - perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i ./$out_dir/contigs.fasta -o $prefix.assembly.$assembler.fa + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/scaffolds.fasta -o $prefix.assembly.$assembler.fa +elif [[ "$assembler" == "wtdbg2" ]] +then + mkdir $out_dir + cd $out_dir + $wtdbg2_dir/wtdbg2 -t $threads -L 5000 -i ./../$long_reads -fo $prefix + $wtdbg2_dir/wtpoa-cns -t $threads -i $prefix.ctg.lay.gz -fo $prefix.ctg.lay.fa + cd .. + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/$prefix.ctg.lay.fa -o $prefix.assembly.$assembler.fa elif [[ "$assembler" == "smartdenovo" ]] then mkdir $out_dir @@ -95,7 +103,7 @@ then maxThreads=$threads \ genomeSize=$genome_size \ gnuplot=$gnuplot_dir/gnuplot \ - -${reads_type} $long_reads \ + -${long_reads_type} $long_reads \ # $customized_canu_parameters if [[ "$long_reads_type" == "pacbio-raw" ]] @@ -116,7 +124,23 @@ then -g $genome_size \ --${long_reads_type} $out_dir/canu/$prefix.correctedReads.fasta.gz \ -i 2 - perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i ./$out_dir/flye/contigs.fasta -o $prefix.assembly.$assembler.fa + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/flye/scaffolds.fasta -o $prefix.assembly.$assembler.fa +elif [[ "$assembler" == "canu-wtdbg2" ]] +then + $canu_dir/canu -correct -p $prefix -d $out_dir/canu \ + useGrid=false \ + maxThreads=$threads \ + genomeSize=$genome_size \ + gnuplot=$gnuplot_dir/gnuplot \ + -${long_reads_type} $long_reads \ + # $customized_canu_parameters + + mkdir -p $out_dir/wtdbg2 + cd $out_dir/wtdbg2 + $wtdbg2_dir/wtdbg2 -t $threads -L 5000 -i ./../canu/$prefix.correctedReads.fasta.gz -fo $prefix + $wtdbg2_dir/wtpoa-cns -t $threads -i $prefix.ctg.lay.gz -fo $prefix.ctg.lay.fa + cd ../.. + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/wtdbg2/$prefix.ctg.lay.fa -o $prefix.assembly.$assembler.fa elif [[ "$assembler" == "canu-smartdenovo" ]] then $canu_dir/canu -correct -p $prefix -d $out_dir/canu \ @@ -129,9 +153,9 @@ then mkdir -p $out_dir/smartdenovo cd $out_dir/smartdenovo - $smartdenovo_dir/smartdenovo.pl -p $prefix -t $threads -c 1 $out_dir/canu/$prefix.correctedReads.fasta.gz > $prefix.mak + $smartdenovo_dir/smartdenovo.pl -p $prefix -t $threads -c 1 ./../canu/$prefix.correctedReads.fasta.gz > $prefix.mak make -f $prefix.mak - cd .. + cd ../.. perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/smartdenovo/$prefix.dmo.cns -o $prefix.assembly.$assembler.fa fi @@ -168,13 +192,10 @@ fi # clean up intermediate files if [[ $debug == "no" ]] then - if [[ "$reads_type" == "nanopore-raw" || "$reads_type" == "nanopore-corrected" ]] - then - rm reads.cleaned.fastq.gz - fi rm *.delta rm *.delta_filter rm ref_genome.fa + rm ref_genome.fa.fai if [[ $vcf == "yes" ]] then rm *.filter.coords diff --git a/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.2.sh b/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.2.sh index 0e4da41..a7e3aec 100755 --- a/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.2.sh +++ b/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.2.sh @@ -12,6 +12,7 @@ prefix="SK1" # The file name prefix for the output files. vcf="yes" # Whether to generate a vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome. Default = "yes". dotplot="yes" # Whether to plot genome-wide dotplot based on the comparison with the reference genome below. Use "yes" if prefer to plot, otherwise use "no". Default = "yes". ref_genome_raw="./../00.Ref_Genome/S288C.ASM205763v1.fa" # The path of the raw reference genome, only needed when dotplot="yes" or vcf="yes". +threads=1 # The number of threads to use. Default = 1. debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no". ####################################### @@ -46,13 +47,13 @@ then fi # make the comparison between the assembled genome and the reference genome -$mummer_dir/nucmer --maxmatch --nosimplify -p $prefix.assembly.final $ref_genome_raw $prefix.assembly.final.fa -$mummer_dir/delta-filter -m $prefix.assembly.final.delta > $prefix.assembly.final.delta_filter +$mummer_dir/nucmer -t $threads --maxmatch --nosimplify -p $prefix.assembly.final $ref_genome_raw $prefix.assembly.final.fa +$mummer_dir/delta-filter -m $prefix.assembly.final.delta > $prefix.assembly.final.delta_filter # generate the vcf output if [[ $vcf == "yes" ]] then - $mummer_dir/show-coords -b -T -r -c -l -d $prefix.assembly.final.delta_filter > $prefix.assembly.final.filter.coords + $mummer_dir/show-coords -b -T -r -c -l -d $prefix.assembly.final.delta_filter > $prefix.assembly.final.filter.coords $mummer_dir/show-snps -C -T -l -r $prefix.assembly.final.delta_filter > $prefix.assembly.final.filter.snps perl $LRSDAY_HOME/scripts/mummer2vcf.pl -r ref_genome.fa -i $prefix.assembly.final.filter.snps -t SNP -p $prefix.assembly.final.filter perl $LRSDAY_HOME/scripts/mummer2vcf.pl -r ref_genome.fa -i $prefix.assembly.final.filter.snps -t INDEL -p $prefix.assembly.final.filter @@ -75,8 +76,8 @@ if [[ $debug == "no" ]] then rm *.delta rm *.delta_filter - # rm ref_genome.fa - # rm ref_genome.fa.fai + rm ref_genome.fa + rm ref_genome.fa.fai if [[ $vcf == "yes" ]] then rm *.filter.coords diff --git a/README.md b/README.md index eaa2811..a83afb7 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,16 @@ # LRSDAY + **LRSDAY: Long-read Sequencing Data Analysis for Yeasts** A highly transparent, automated and powerful computational framework for high-quality genome assembly and annotation. -![LRSDAY_flowchart](https://github.com/yjx1217/LRSDAY/blob/master/LRSDAY_flowchart.png) +[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) ## Description Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast, *Saccharomyces cerevisiae*, has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here we present LRSDAY, the first one-stop solution to streamline this process. LRSDAY can produce chromosome-level end-to-end genome assembly and comprehensive annotations for various genomic features (including centromeres, protein-coding genes, tRNAs, transposable elements and telomere-associated elements) that are ready for downstream analysis. Although tailored for *S. cerevisiae*, we designed LRSDAY to be highly modular and customizable, making it adaptable for virtually any eukaryotic organisms. +![LRSDAY_flowchart](https://github.com/yjx1217/LRSDAY/blob/master/LRSDAY_flowchart.png) + ## Citations Jia-Xing Yue & Gianni Liti. (2018) Long-read sequencing data analysis for yeasts. *Nature Protocols*, 13:1213–1231. @@ -15,6 +18,7 @@ Jia-Xing Yue & Gianni Liti. (2018) Long-read sequencing data analysis for yeasts Jia-Xing Yue, Jing Li, Louise Aigrain, Johan Hallin, Karl Persson, Karen Oliver, Anders Bergström, Paul Coupland, Jonas Warringer, Marco Cosentino Lagomarsino, Gilles Fischer, Richard Durbin, Gianni Liti. (2017) Contrasting evolutionary genome dynamics between domesticated and wild yeasts. *Nature Genetics*, 49:913-924. ## Release history +* v1.3.0 Released on 2018/11/13 * v1.2.0 Released on 2018/10/15 * v1.1.0 Released on 2018/07/11 * v1.0.0 Released on 2018/02/04 diff --git a/install_dependencies.sh b/install_dependencies.sh index 551c2d5..dfd821e 100755 --- a/install_dependencies.sh +++ b/install_dependencies.sh @@ -1,23 +1,25 @@ #!/bin/bash -# last update: 2018/08/13 +# last update: 2018/10/26 set -e -o pipefail LRSDAY_HOME=$(pwd) BUILD="build" -SRA_VERSION="2.9.2" # "2.8.2-1" -PORECHOP_VERSION="0.2.3" # "0.2.3" -PORECHOP_GITHUB_COMMIT_VERSION="289d5dc" # committed on 2017.12.06 +SRA_VERSION="2.9.2" # "2.9.2" +PORECHOP_VERSION="0.2.4" # "0.2.3" +PORECHOP_GITHUB_COMMIT_VERSION="109e437" # committed on 2018.10.19 FILTLONG_VERSION="0.2.0" FILTLONG_GITHUB_COMMIT_VERSION="d1bb46d" # committed on 2018.05.11 -MINIMAP2_VERSION="2.12" -CANU_VERSION="1.7.1" # "1.5" -FLYE_VERSION="2.3.6" # "2.3.3" +MINIMAP2_VERSION="2.13" +CANU_VERSION="1.8" # "1.7.1" +FLYE_VERSION="2.3.6" # "2.3.6" +WTDBG2_VERSION="2.2" +WTDBG2_GITHUB_COMMIT_VERSION="db346b3" # committed on 2018.11.05 SMARTDENOVO_VERSION="" # not available, so we use the github comit hash below for version control SMARTDENOVO_GITHUB_COMMIT_VERSION="5cc1356" # committed on 2018.02.19 RAGOUT_VERSION="2.1.1" -#QUAST_VERSION="5.0.0" # one of its dependency needs "csh" to be pre-installed +#QUAST_VERSION="5.0.1" # one of its dependency needs "csh" to be pre-installed HDF_VERSION="1.10.1" SONLIB_VERSION="" # not available, so we use the github comit hash below for version control SONLIB_GITHUB_COMMIT_VERSION="1afbd97" # committed on 2017.08.09 @@ -26,15 +28,15 @@ HAL_GITHUB_COMMIT_VERSION="a2ad656" # committed on 2017.09.09 MUMMER_VERSION="4.0.0beta2" GNUPLOT_VERSION="4.6.6" BEDTOOLS_VERSION="2.27.1" -SPADES_VERSION="3.12.0" # "3.10.1" +SPADES_VERSION="3.13.0" # "3.12.0" PRODIGAL_VERSION="2.6.3" CAP_VERSION="" # see http://seq.cs.iastate.edu/cap3.html BWA_VERSION="0.7.17" # "0.7.15" SAMTOOLS_VERSION="1.9" #"1.3" CIRCLATOR_VERSION="1.5.5" # "1.5.1" TRIMMOMATIC_VERSION="0.36" -GATK_VERSION="3.8" -PICARD_VERSION="2.18.12" # "2.18.4" +GATK_VERSION="3.6-6" +PICARD_VERSION="2.18.15" # "2.18.12" PILON_VERSION="1.22" EXONERATE_VERSION="2.2.0" BLAST_VERSION="2.2.31" @@ -45,10 +47,11 @@ RAPSEARCH_VERSION="2.24" TRNASCAN_VERSION="1.3.1" SNOSCAN_VERSION="0.9.1" REPEATMASKER_VERSION="open-4-0-7" +TRF_VERSION="409" REANNOTATE_VERSION="17.03.2015-LongQueryName" CLUSTALW_VERSION="2.1" MUSCLE_VERSION="3.8.31" -HMMER_VERSION="3.1b2" +HMMER_VERSION="3.2.1" BAMTOOLS_VERSION="2.4.2" AUGUSTUS_VERSION="3.2.3" #AUGUSTUS_GITHUB_COMMIT_VERSION="79960C5" @@ -56,10 +59,10 @@ EVM_VERSION="1.1.1" PROTEINORTHO_VERSION="5.16b" # "5.16" MAKER_VERSION="3.00.0-beta" MINICONDA2_VERSION="4.5.11" -PB_ASSEMBLY_VERSION="0.0.1" +PB_ASSEMBLY_VERSION="0.0.2" BAX2BAM_VERSION="0.0.9" NANOPOLISH_VERSION="0.10.2" -NANOPOLISH_GITHUB_COMMIT_VERSION="f1de746" # committed on 2018.09.13 +NANOPOLISH_GITHUB_COMMIT_VERSION="d7c09ab" # committed on 2018.11.02 PARALLEL_VERSION="20180722" # for MFannot EMBOSS_VERSION="6.5.7" @@ -74,7 +77,8 @@ RNAFINDER_GITHUB_COMMIT_VERSION="579dc58" # committed on 2016.12.07 MF2SQN_GITHUB_COMMIT_VERSION="6faf9f4" # committed on 2016.12.07 GRAB_FASTA_GITHUB_COMMIT_VERSION="accd32d" # committed on 2017.02.14 MFANNOT_DATA_GITHUB_COMMIT_VERSION="b039ac5" # committed on 2016.12.07 -MFANNOT_GITHUB_COMMIT_VERSION="a4a8408" # committed on 2018.09.21 +MFANNOT_VERSION="1.35" +MFANNOT_GITHUB_COMMIT_VERSION="6472b97" # committed on 2018.10.31 # downloading URLs for dependencies SRA_DOWNLOAD_URL="https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz" @@ -83,6 +87,7 @@ FILTLONG_DOWNLOAD_URL="https://github.com/rrwick/Filtlong.git" MINIMAP2_DOWNLOAD_URL="https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2" CANU_DOWNLOAD_URL="https://github.com/marbl/canu/archive/v${CANU_VERSION}.tar.gz" FLYE_DOWNLOAD_URL="https://github.com/fenderglass/Flye/archive/${FLYE_VERSION}.tar.gz" +WTDBG2_DOWNLOAD_URL="https://github.com/ruanjue/wtdbg2.git" SMARTDENOVO_DOWNLOAD_URL="https://github.com/ruanjue/smartdenovo" #QUAST_DOWNLOAD_URL="https://downloads.sourceforge.net/project/quast/quast-${QUAST_VERSION}.tar.gz" RAGOUT_DOWNLOAD_URL="https://github.com/fenderglass/Ragout/archive/${RAGOUT_VERSION}.tar.gz" @@ -112,10 +117,12 @@ RAPSEARCH_DOWNLOAD_URL="https://sourceforge.net/projects/rapsearch2/files/RAPSea TRNASCAN_DOWNLOAD_URL="http://eddylab.org/software/tRNAscan-SE/tRNAscan-SE.tar.gz" SNOSCAN_DOWNLOAD_URL="http://eddylab.org/software/snoscan/snoscan.tar.gz" REPEATMASKER_DOWNLOAD_URL="http://repeatmasker.org/RepeatMasker-${REPEATMASKER_VERSION}.tar.gz" +TRF_DOWNLOAD_URL="http://tandem.bu.edu/trf/downloads/trf${TRF_VERSION}.linux64" REANNOTATE_DOWNLOAD_URL="https://github.com/yjx1217/REannotate_LongQueryName/archive/version_${REANNOTATE_VERSION}.tar.gz" CLUSTALW_DOWNLOAD_URL="http://www.clustal.org/download/${CLUSTALW_VERSION}/clustalw-${CLUSTALW_VERSION}.tar.gz" MUSCLE_DOWNLOAD_URL="http://www.drive5.com/muscle/downloads${MUSCLE_VERSION}/muscle${MUSCLE_VERSION}_i86linux64.tar.gz" -HMMER_DOWNLOAD_URL="http://eddylab.org/software/hmmer3/${HMMER_VERSION}/hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz" +#HMMER_DOWNLOAD_URL="http://eddylab.org/software/hmmer3/${HMMER_VERSION}/hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz" +HMMER_DOWNLOAD_URL="http://eddylab.org/software/hmmer/hmmer-${HMMER_VERSION}.tar.gz" BAMTOOLS_DOWNLOAD_URL="https://github.com/pezmaster31/bamtools/archive/v${BAMTOOLS_VERSION}.tar.gz" AUGUSTUS_DOWNLOAD_URL="http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-${AUGUSTUS_VERSION}.tar.gz" #AUGUSTUS_DOWNLOAD_URL="https://github.com/Gaius-Augustus/Augustus.git" @@ -286,6 +293,16 @@ cd .. flye_dir="$build_dir/Flye-${FLYE_VERSION}/bin" rm Flye-${FLYE_VERSION}.tar.gz +# --------------- wtdbg2 ------------------ +cd $build_dir +echo "Download wtdbg2-v${WTDBG2_VERSION}" +git clone $WTDBG2_DOWNLOAD_URL +cd wtdbg2 +git reset --hard $WTDBG2_GITHUB_COMMIT_VERSION +C_INCLUDE_PATH="" +make +wtdbg2_dir="$build_dir/wtdbg2" + # --------------- smartdenovo ------------------ cd $build_dir echo "Download smartdenovo-v${SMARTDENOVO_VERSION}" @@ -583,8 +600,23 @@ echo "Download Repeatmasker-v${REPEATMASKER_VERSION}" download $REPEATMASKER_DOWNLOAD_URL "RepeatMasker-${REPEATMASKER_VERSION}.tar.gz" tar -zxf RepeatMasker-${REPEATMASKER_VERSION}.tar.gz repeatmasker_dir="$build_dir/RepeatMasker" +cd $repeatmasker_dir +echo "Download and setup RepBase library" +REPBASE_VERSION="20170127" +wget https://github.com/yjx1217/RMRB/raw/master/RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz +tar xzf RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz +rm RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz +cd .. rm RepeatMasker-${REPEATMASKER_VERSION}.tar.gz +# --------------- TRF ------------------ +cd $repeatmasker_dir +echo "Download TRF-v${TRF_VERSION}" +download $TRF_DOWNLOAD_URL "trf${TRF_VERSION}.linux64" +mv trf${TRF_VERSION}.linux64 trf +chmod 755 trf +trf_dir=$repeatmasker_dir + # --------------- REannotate ------------------ cd $build_dir echo "Download REannotate-v${REANNOTATE_VERSION}" @@ -625,7 +657,16 @@ cd $build_dir echo "Download hmmer-v${HMMER_VERSION}" download $HMMER_DOWNLOAD_URL "hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz" tar -zxf hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz -hmmer_dir="$build_dir/hmmer-${HMMER_VERSION}-linux-intel-x86_64/binaries" +hmmer_dir="$build_dir/hmmer-${HMMER_VERSION}" +cd $hmmer_dir +./configure --prefix=$hmmer_dir +make +make install +cd easel +make install +cd .. +cd .. +hmmer_dir="$build_dir/hmmer-${HMMER_VERSION}/bin" rm hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz # --------------- bamtools ------------------ @@ -698,6 +739,9 @@ rm proteinortho_v${PROTEINORTHO_VERSION}.tar.gz cd $build_dir echo "Create GATK3 folder for users' manual installation" mkdir GATK3 +cd GATK3 +wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/GenomeAnalysisTK.jar +chmod 755 GenomeAnalysisTK.jar gatk_dir="$build_dir/GATK3" # --------------- MAKER ----------------- @@ -907,6 +951,7 @@ echo "export filtlong_dir=${filtlong_dir}" >> env.sh echo "export minimap2_dir=${minimap2_dir}" >> env.sh echo "export canu_dir=${canu_dir}" >> env.sh echo "export flye_dir=${flye_dir}" >> env.sh +echo "export wtdbg2_dir=${wtdbg2_dir}" >> env.sh echo "export smartdenovo_dir=${smartdenovo_dir}" >> env.sh #echo "export quast_dir=${quast_dir}" >> env.sh echo "export ragout_dir=${ragout_dir}" >> env.sh @@ -935,7 +980,7 @@ echo "export rapsearch_dir=${rapsearch_dir}" >> env.sh echo "export trnascan_dir=${trnascan_dir}" >> env.sh echo "export snoscan_dir=${snoscan_dir}" >> env.sh echo "export repeatmasker_dir=${repeatmasker_dir}" >> env.sh -echo "export trf_dir=${repeatmasker_dir}" >> env.sh +echo "export trf_dir=${trf_dir}" >> env.sh echo "export reannotate_dir=${reannotate_dir}" >> env.sh echo "export clustalw_dir=${clustalw_dir}" >> env.sh echo "export muscle_dir=${muscle_dir}" >> env.sh @@ -1004,15 +1049,12 @@ echo "or the GNU General Public License developed by the Free Software Foundatio echo "MAKER is not available for commercial use without a license." echo "If wishing to license MAKER for commercial use, please contact Aaron Duffy at University of Utah TVC by email at Aaron.Duffy@tvc.utah.edu." echo "" -echo "5) The following dependencies need manual registration and installation:" -echo "5.1) Download GATK (v${GATK_VERSION}) from \"https://software.broadinstitute.org/gatk/download/archive\". Registration might be needed." -echo "Once downloaded, use the command \"tar -xjf GenomeAnalysisTK-v${GATK_VERSION}.tar.bz2\" to uncompress the file and" -echo "move the resulting \"GenomeAnalysisTK.jar\" file into the directory $gatk_dir" -echo "" -echo "5.2) RepeatMasker need manual configuration." -echo "Please refer to our user manual or the protocol paper describing LRSDAY to configure RepeatMasker." +echo "5) RepeatMasker need manual configuration." +echo "Please refer to our latest LRSDAY Manual for proper configuration of RepeatMasker." echo "When making configuration for RepeatMasker, please use $trf_dir for configuring TRF and use $rmblast_dir for configuring rmblast." echo "" +echo "6) The RepeatMasker dependency library Repbase (https://www.girinst.org/repbase/) will be switched to subscription-based model soon. Please consider subscribing this library for keeping up with the latest version of their product." +echo "" echo "#########################################################" diff --git a/pipelines/LRSDAY.01.Long-read-based_Genome_Assembly.sh b/pipelines/LRSDAY.01.Long-read-based_Genome_Assembly.sh index 16f7956..222af03 100755 --- a/pipelines/LRSDAY.01.Long-read-based_Genome_Assembly.sh +++ b/pipelines/LRSDAY.01.Long-read-based_Genome_Assembly.sh @@ -11,8 +11,8 @@ prefix="SK1" # The file name prefix for the output files. long_reads="./../00.Long_Reads/SK1.filtered_subreads.fastq.gz" # The file path of the long reads file (in fastq or fastq.gz format). long_reads_type="pacbio-raw" # The long reads data type. Use "pacbio-raw" or "pacbio-corrected" or "nanopore-raw" or "nanopore-corrected". Default = "pacbio-raw" for the testing example genome_size="12.5m" # The estimated genome size with the format of [g|m|k], e.g. 12.5m for 12.5 Mb. Default = "12.5m". -assembler="canu" # The long-read assembler: Use "canu" or "flye" or "smartdenovo" or "canu-flye" or "canu-smartdenovo". For "canu-flye" and "canu-smartdenovo", the assembler canu is used first to generate error-corrected reads from the raw reads and then the assembler flye/smartdenovo is used to assemble the genome. Based on our test, assembler="canu" generally gives the best result but will take substantially longer time than the other options. -customized_canu_parameters="-correctedErrorRate=0.04" # For assembler="canu" only. Users can set customized Canu assembly parameters here or simply leave it empty like "" to use Canu's default assembly parameter. For example you could set "-correctedErrorRate=0.04" for high coverage (>60X) PacBio data and "-correctedErrorRate=0.12 -overlapper=mhap -utgReAlign=true" for high coverage (>60X) Nanopore data to improve the assembly speed. More than one customized parameters can be set here as long as they are separeted by space (e.g. "-option1=XXX -option2=YYY -option3=ZZZ"). Please consult Canu's manual "http://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak" for advanced customization settings. Default = "-correctedErrorRate=0.04" for the testing example. +assembler="canu" # The long-read assembler: Use "canu" or "flye" or "wtdbg2" or "smartdenovo" or "canu-flye" or "canu-wtdbg2" or "canu-smartdenovo". For "canu-flye", "canu-wtdbg2", and "canu-smartdenovo", the assembler canu is used first to generate error-corrected reads from the raw reads and then the assembler flye/wtdbg2/smartdenovo is used to assemble the genome. Based on our test, assembler="canu" generally gives the best result but will take substantially longer time than the other options. +customized_canu_parameters="-correctedErrorRate=0.04" # For assembler="canu" only. Users can set customized Canu assembly parameters here or simply leave it empty like "" to use Canu's default assembly parameter. For example you could set "-correctedErrorRate=0.04" for high coverage (>60X) PacBio data and "-overlapper=mhap -utgReAlign=true" for high coverage (>60X) Nanopore data to improve the assembly speed. More than one customized parameters can be set here as long as they are separeted by space (e.g. "-option1=XXX -option2=YYY -option3=ZZZ"). Please consult Canu's manual "http://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak" for advanced customization settings. Default = "-correctedErrorRate=0.04" for the testing example. threads=1 # The number of threads to use. Default = 1. vcf="yes" # Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Otherwise use "no". Default = "yes". dotplot="yes" # Use "yes" if prefer to plot genome-wide dotplot based on the comparison with the reference genome below. Otherwise use "no". Default = "yes". @@ -59,25 +59,33 @@ then -${long_reads_type} $long_reads \ $customized_canu_parameters - perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i ./$out_dir/$prefix.contigs.fasta -o $prefix.assembly.$assembler.fa + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/$prefix.contigs.fasta -o $prefix.assembly.$assembler.fa elif [[ "$assembler" == "flye" ]] then if [[ "$long_reads_type" == "pacbio-corrected" ]] then - reads_type="pacbio-corr" + long_reads_type="pacbio-corr" elif [[ "$long_reads_type" == "nanopore-raw" ]] then - reads_type="nano-raw" + long_reads_type="nano-raw" elif [[ "$long_reads_type" == "nanopore-corrected" ]] then - reads_type="nano-corr" + long_reads_type="nano-corr" fi - $flye_new_dir/flye -o $out_dir \ + $flye_dir/flye -o $out_dir \ -t $threads \ -g $genome_size \ --${long_reads_type} $long_reads \ -i 2 - perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i ./$out_dir/contigs.fasta -o $prefix.assembly.$assembler.fa + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/scaffolds.fasta -o $prefix.assembly.$assembler.fa +elif [[ "$assembler" == "wtdbg2" ]] +then + mkdir $out_dir + cd $out_dir + $wtdbg2_dir/wtdbg2 -t $threads -L 5000 -i ./../$long_reads -fo $prefix + $wtdbg2_dir/wtpoa-cns -t $threads -i $prefix.ctg.lay.gz -fo $prefix.ctg.lay.fa + cd .. + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/$prefix.ctg.lay.fa -o $prefix.assembly.$assembler.fa elif [[ "$assembler" == "smartdenovo" ]] then mkdir $out_dir @@ -95,7 +103,7 @@ then maxThreads=$threads \ genomeSize=$genome_size \ gnuplot=$gnuplot_dir/gnuplot \ - -${reads_type} $long_reads \ + -${long_reads_type} $long_reads \ # $customized_canu_parameters if [[ "$long_reads_type" == "pacbio-raw" ]] @@ -116,7 +124,23 @@ then -g $genome_size \ --${long_reads_type} $out_dir/canu/$prefix.correctedReads.fasta.gz \ -i 2 - perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i ./$out_dir/flye/contigs.fasta -o $prefix.assembly.$assembler.fa + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/flye/scaffolds.fasta -o $prefix.assembly.$assembler.fa +elif [[ "$assembler" == "canu-wtdbg2" ]] +then + $canu_dir/canu -correct -p $prefix -d $out_dir/canu \ + useGrid=false \ + maxThreads=$threads \ + genomeSize=$genome_size \ + gnuplot=$gnuplot_dir/gnuplot \ + -${long_reads_type} $long_reads \ + # $customized_canu_parameters + + mkdir -p $out_dir/wtdbg2 + cd $out_dir/wtdbg2 + $wtdbg2_dir/wtdbg2 -t $threads -L 5000 -i ./../canu/$prefix.correctedReads.fasta.gz -fo $prefix + $wtdbg2_dir/wtpoa-cns -t $threads -i $prefix.ctg.lay.gz -fo $prefix.ctg.lay.fa + cd ../.. + perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/wtdbg2/$prefix.ctg.lay.fa -o $prefix.assembly.$assembler.fa elif [[ "$assembler" == "canu-smartdenovo" ]] then $canu_dir/canu -correct -p $prefix -d $out_dir/canu \ @@ -129,9 +153,9 @@ then mkdir -p $out_dir/smartdenovo cd $out_dir/smartdenovo - $smartdenovo_dir/smartdenovo.pl -p $prefix -t $threads -c 1 $out_dir/canu/$prefix.correctedReads.fasta.gz > $prefix.mak + $smartdenovo_dir/smartdenovo.pl -p $prefix -t $threads -c 1 ./../canu/$prefix.correctedReads.fasta.gz > $prefix.mak make -f $prefix.mak - cd .. + cd ../.. perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/smartdenovo/$prefix.dmo.cns -o $prefix.assembly.$assembler.fa fi @@ -168,13 +192,10 @@ fi # clean up intermediate files if [[ $debug == "no" ]] then - if [[ "$reads_type" == "nanopore-raw" || "$reads_type" == "nanopore-corrected" ]] - then - rm reads.cleaned.fastq.gz - fi rm *.delta rm *.delta_filter rm ref_genome.fa + rm ref_genome.fa.fai if [[ $vcf == "yes" ]] then rm *.filter.coords diff --git a/pipelines/LRSDAY.07.Supervised_Final_Assembly.2.sh b/pipelines/LRSDAY.07.Supervised_Final_Assembly.2.sh index 0e4da41..a7e3aec 100755 --- a/pipelines/LRSDAY.07.Supervised_Final_Assembly.2.sh +++ b/pipelines/LRSDAY.07.Supervised_Final_Assembly.2.sh @@ -12,6 +12,7 @@ prefix="SK1" # The file name prefix for the output files. vcf="yes" # Whether to generate a vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome. Default = "yes". dotplot="yes" # Whether to plot genome-wide dotplot based on the comparison with the reference genome below. Use "yes" if prefer to plot, otherwise use "no". Default = "yes". ref_genome_raw="./../00.Ref_Genome/S288C.ASM205763v1.fa" # The path of the raw reference genome, only needed when dotplot="yes" or vcf="yes". +threads=1 # The number of threads to use. Default = 1. debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no". ####################################### @@ -46,13 +47,13 @@ then fi # make the comparison between the assembled genome and the reference genome -$mummer_dir/nucmer --maxmatch --nosimplify -p $prefix.assembly.final $ref_genome_raw $prefix.assembly.final.fa -$mummer_dir/delta-filter -m $prefix.assembly.final.delta > $prefix.assembly.final.delta_filter +$mummer_dir/nucmer -t $threads --maxmatch --nosimplify -p $prefix.assembly.final $ref_genome_raw $prefix.assembly.final.fa +$mummer_dir/delta-filter -m $prefix.assembly.final.delta > $prefix.assembly.final.delta_filter # generate the vcf output if [[ $vcf == "yes" ]] then - $mummer_dir/show-coords -b -T -r -c -l -d $prefix.assembly.final.delta_filter > $prefix.assembly.final.filter.coords + $mummer_dir/show-coords -b -T -r -c -l -d $prefix.assembly.final.delta_filter > $prefix.assembly.final.filter.coords $mummer_dir/show-snps -C -T -l -r $prefix.assembly.final.delta_filter > $prefix.assembly.final.filter.snps perl $LRSDAY_HOME/scripts/mummer2vcf.pl -r ref_genome.fa -i $prefix.assembly.final.filter.snps -t SNP -p $prefix.assembly.final.filter perl $LRSDAY_HOME/scripts/mummer2vcf.pl -r ref_genome.fa -i $prefix.assembly.final.filter.snps -t INDEL -p $prefix.assembly.final.filter @@ -75,8 +76,8 @@ if [[ $debug == "no" ]] then rm *.delta rm *.delta_filter - # rm ref_genome.fa - # rm ref_genome.fa.fai + rm ref_genome.fa + rm ref_genome.fa.fai if [[ $vcf == "yes" ]] then rm *.filter.coords