version update for LRSDAY: v1.5.0 -> v1.6.0

yjx1217 · Oct 3, 2019 · c019d6e · c019d6e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,12 +7,27 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+## [1.6.0] - 2019-10-03
+### Added
+- Supports for canu-triobinning assembly mode for phased hybrid genome assembly.
+- Supports for new alternative long-read-assemblers: Ra and Shasta.
+- Supports for new alternative long-read-based polishers: Racon, Medaka, and MarginPolish.
+- Supports for new alternative reference-genome-based scaffolder: RaGOO.
+
+### Changed
+- Better robustness for the dependency installation script.
+- Better treatment for identifying mitochondrial contigs when they contain assembly gaps.
+- Minor adjustment for a few task-specific directory names.
+- Software version updates for a number of dependencies.
+### Fixed
+- A bug that will disrupt long-read-based assembly run when assembler="canu-flye", "canu-wtdbg2" or "canu-smartdenovo" because of deleting a non-existing file.
+
 ## [1.5.0] - 2019-05-13
 ### Added
 - Supports for native ONT nanopore basecalling, demultiplexing, and read profile plotting.
 - An lite-weight bash script for generating dotplot for any pairs of fasta files.
 ### Changed
-- Better robustness for the dependency installation script. 
+- Better robustness for the dependency installation script.
 - Reducing the requirements of setting output prefix by assuming the same prefix was used across different modules.
 - Setting adjustment for long-read filtering and downsampling.
 - Applying read filtering/downsampling for the testing example.

diff --git a/Example_Outputs/SK1.assembly.final.fa.gz b/Example_Outputs/SK1.assembly.final.fa.gz
diff --git a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz
diff --git a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz
diff --git a/Example_Outputs/SK1.assembly.final.filter.pdf b/Example_Outputs/SK1.assembly.final.filter.pdf
diff --git a/Example_Outputs/SK1.final.cds.fa.gz b/Example_Outputs/SK1.final.cds.fa.gz
diff --git a/Example_Outputs/SK1.final.gff3.gz b/Example_Outputs/SK1.final.gff3.gz
diff --git a/Example_Outputs/SK1.final.manual_check.list b/Example_Outputs/SK1.final.manual_check.list
@@ -192,59 +192,50 @@ SK1_G0052670|SK1_G0052670.mRNA.1	unexpected start & end codons based on standard
 SK1_G0052680|SK1_G0052680.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0052700|SK1_G0052700.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0052730|SK1_G0052730.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_G0053030|SK1_G0053030.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0053120|SK1_G0053120.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0053520|SK1_G0053520.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1
 SK1_G0053650|SK1_G0053650.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_G0054250|SK1_G0054250.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0054350|SK1_G0054350.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0054540|SK1_G0054540.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_G0054900|SK1_G0054900.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055070|SK1_G0055070.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055130|SK1_G0055130.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055210|SK1_G0055210.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055220|SK1_G0055220.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0055480|SK1_G0055480.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_G0055760|SK1_G0055760.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055840|SK1_G0055840.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0055850|SK1_G0055850.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0055940|SK1_G0055940.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0056240|SK1_G0056240.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0056440|SK1_G0056440.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0056590|SK1_G0056590.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057200|SK1_G0057200.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1
-SK1_G0057230|SK1_G0057230.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0053830|SK1_G0053830.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0054270|SK1_G0054270.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0054370|SK1_G0054370.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0054560|SK1_G0054560.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0055100|SK1_G0055100.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0055160|SK1_G0055160.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0055240|SK1_G0055240.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0055500|SK1_G0055500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0055970|SK1_G0055970.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0056270|SK1_G0056270.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0057280|SK1_G0057280.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057310|SK1_G0057310.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057370|SK1_G0057370.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1
-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_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_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_G0057440|SK1_G0057440.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	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057730|SK1_G0057730.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0057330|SK1_G0057330.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_G0057410|SK1_G0057410.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0057470|SK1_G0057470.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1
+SK1_G0057490|SK1_G0057490.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_G0057540|SK1_G0057540.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	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_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_G0057860|SK1_G0057860.mRNA.1	incorrect CDS length
+SK1_G0057890|SK1_G0057890.mRNA.1	incorrect CDS length
 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_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_G0058000|SK1_G0058000.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0058010|SK1_G0058010.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0058060|SK1_G0058060.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0058100|SK1_G0058100.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1
-SK1_G0058190|SK1_G0058190.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058200|SK1_G0058200.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058220|SK1_G0058220.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058230|SK1_G0058230.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 & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058370|SK1_G0058370.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058410|SK1_G0058410.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0058460|SK1_G0058460.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058640|SK1_G0058640.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
+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_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_G0058100|SK1_G0058100.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
+SK1_G0058110|SK1_G0058110.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
+SK1_G0058160|SK1_G0058160.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
+SK1_G0058200|SK1_G0058200.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1
+SK1_G0058290|SK1_G0058290.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058300|SK1_G0058300.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058320|SK1_G0058320.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058330|SK1_G0058330.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058340|SK1_G0058340.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058350|SK1_G0058350.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1
+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_G0058550|SK1_G0058550.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058760|SK1_G0058760.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
 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

diff --git a/Example_Outputs/SK1.final.pep.fa.gz b/Example_Outputs/SK1.final.pep.fa.gz
diff --git a/Example_Outputs/SK1.final.trimmed_cds.fa.gz b/Example_Outputs/SK1.final.trimmed_cds.fa.gz
diff --git a/LRSDAY_flowchart.png b/LRSDAY_flowchart.png
diff --git a/Manual.pdf b/Manual.pdf
diff --git a/Project_Template/00.Long_Reads/LRSDAY.00.Summary_Report_for_Long_Reads.sh b/Project_Template/00.Long_Reads/LRSDAY.00.Summary_Report_for_Long_Reads.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+set -e -o pipefail
+#######################################
+# load environment variables for LRSDAY
+source ./../../env.sh
+
+#######################################
+# set project-specific variables
+long_reads_in_fastq="SK1.filtered_subreads.fastq.gz" # The fastq file of long-reads (in fastq or fastq.gz format). Default = "SK1.filtered_subreads.fastq.gz"
+prefix="SK1" # The file name prefix for output files of the testing example. 
+threads=1 # The number of threads to use. Default = "1".
+
+#######################################
+# process the pipeline
+
+#source $nanoplot_dir/activate
+$nanoplot_dir/NanoPlot \
+    --threads $threads \
+    --fastq $long_reads_in_fastq \
+    --minlength 0 \
+    --drop_outliers \
+    --N50 \
+    -o "${prefix}_Long_Reads_Summary_Report_out"
+
+############################
+# checking bash exit status
+if [[ $? -eq 0 ]]
+then
+    echo "" 
+    echo "LRSDAY message: This bash script has been successfully processed! :)"
+    echo ""
+    echo ""
+    exit 0
+fi
+############################
diff --git a/...Genome/LRSDAY.00.Prepare_Sc_Ref_Genome.sh → .../LRSDAY.00.Prepare_Sc_Reference_Genome.sh b/...Genome/LRSDAY.00.Prepare_Sc_Ref_Genome.sh → .../LRSDAY.00.Prepare_Sc_Reference_Genome.sh
diff --git a/...SDAY.00.Retrieve_Sample_Illumina_Reads.sh → ...SDAY.00.Retrieve_Sample_Illumina_Reads.sh b/...SDAY.00.Retrieve_Sample_Illumina_Reads.sh → ...SDAY.00.Retrieve_Sample_Illumina_Reads.sh