I want to assembly all the reads at ones in linux
Hello, I'm new in bioinformatics and I need help please in linux
I have folder contain 109 couple of reads Forward and reverse (218 files) and I want to assembly every couple of reads using spades the name of reads is like this SRR....R.fastq.gz (reverse) SRR...F.fastq.gz (forward)
I need to use for loop to assembly all the reads at ones (because I don't want to repeat the same command 109 times
for example I have four reads file SRR1.F.fastq.gz SRR2.f.fastq.gz SRR1.R.fastq.gz SRR2.R.fastq.gz and I need to take SRR1.F with SRR1.R and so on
Can you help me please
Thank you in advance
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mrmrwinter •
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Bioinfo •
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Bioinfo •
1 answer
In Snakemake:
sample = glob_wildcards("path/{sample}.F.fastq.gz")
rule all:
input: expand("path/spades_out/{sample}/scaffolds.fa", sample=sample)
rule spades:
input:
F = "path/{sample}.F.fastq.gz"
R = "path/{sample}.R.fastq.gz"
output:
"path/spades_out/{sample}/scaffolds.fa"
params:
out = "path/spades_out/{sample}/"
shell:
spades.py -1 {input.F} -2 {input.R} -o {params.out}
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What you need is a pipeline, nextflow, wdl, snakemake. Take a look at https://github.com/nf-core/mag for instance
thank you for your response but i didn't find the page (Page not found )
This question has been asked a lot on the forum. Take a look in the "Similar posts" list at the right hand side, or search the forum via the searchbar/google.
Okay i will look for similar posts thank you