gauravearn / miseq-nextseq-novaseq-genome

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.

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
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany