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miseq-nextseq-novaseq-genome

  • A pure shell assembler that takes only the directory path and does all the cleaning of the reads, mapping, remapping and assembly.
  • From start to finish everything by providing a simple directory path. You dont have to provide anything else just the directory path of the fastq files.
  • It works with MiSeq, NextSeq, NovaSeq. It works with all plant, bacterial and fungal genomes.
shell_command
hi there i am a denovo assembler script which will check your fastq files, \
clean then and assemble them coming from the illumina platform. I take MiSeq, NextSeq,\
NovaSeq reads, you can just clean, or clean and map or clean and assemble.As of the \
current it supports the cleaning through the fastp, mapping through the bowtie2 and \
assembly using the spades I will add more assembler to this interface and also multiple \
assembly configurations. Currently, it supports 45, 55, 65 kmers you can change the \
kmer according to the assembly preferences.\
# if from cleaning only 
main ✗ $ sh genome_cleaner.sh
enter the name of the directory: /Users/gauravsablok/Desktop/GitHub/shell_builder \
do you want to clean the reads:yes \
enter the number of the threads:1 \
do you want to map the reads:no \
enter the name of the bowtie index:no \
do you want to assemble the reads:no \
Processing the cleaning of the reads file from the sequencing runs
fastp --in1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt \
        --out1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
        --in2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text1 \
        --out2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R2 --threads 1 \
# if cleaning to remapping files 
enter the name of the directory: /Users/gauravsablok/Desktop/GitHub/shell_builder \
do you want to clean the reads:yes \
enter the number of the threads:1 \
do you want to map the reads:yes \
enter the name of the bowtie index:gaurav \
do you want to assemble the reads:no \
Processing the cleaning of the reads file from the sequencing runs \
fastp --in1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt \
        --out1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
        --in2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text1 \
        --out2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R2 --threads 1 \
bowtie2-build gaurav gaurav \
bowtie2 -t -x gaurav -p 1 --very-sensitive-local -1 \
       /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
         -2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text3.txt.cleaned.R2 \
                 -S gaurav.sam --no-unal --al-conc gaurav.aligned.fastq \                          
# if from cleaning to assembly configuration \
enter the name of the directory: /Users/gauravsablok/Desktop/GitHub/shell_builder \
do you want to clean the reads:yes \
enter the number of the threads:1 \
do you want to map the reads:yes \
enter the name of the bowtie index:gaurav \
do you want to assemble the reads:yes \
Processing the cleaning of the reads file from the sequencing runs \
fastp --in1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt \
        --out1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
        --in2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text1 \
        --out2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R2 --threads 1 \
bowtie2-build gaurav gaurav \
bowtie2 -t -x gaurav -p 1 --very-sensitive-local -1 \
       /Users/gauravsablok/Desktop/GitHub/shell_builder/text.txt.cleaned.R1 \
         -2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text3.txt.cleaned.R2 \
                 -S gaurav.sam --no-unal --al-conc gaurav.aligned.fastq \
spades.py -1 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.aligned.R1.fastq \
       -2 /Users/gauravsablok/Desktop/GitHub/shell_builder/text.aligned.R2.fastq \
                 --careful --threads 1 --tmp-dir  -k 45,55,65,75 \
                                 -o /Users/gauravsablok/Desktop/GitHub/shell_builder/ \

Gaurav Sablok
University of Potsdam
Potsdam,Germany