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How to perform SOAPdenovo for many samples

Dear Friends,

I need a help. I have 30 paired end reads of 30 samples and I need to assemble it in a single go using SOAPdenovo with a single command. I have already done it one by one but I need a command to perform all the 30 read files at once.

Thank you Michael

assembly
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updated by h.mon h.mon • written by michaelijesse • michaelijesse

Tried anything like looping, GNU parallel or the like?

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written by ATpoint ATpoint

Do you want a single assembly using all 30 samples as input? Or do you want 30 assemblies, but all running in parallel?

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written by h.mon h.mon

1 answer 

#!/bin/bash

for i in `ls *.fastq`
        do
        soapdenovo2 <parameters> $i    &
done

You'll need to set up the config files for each separately though but try that. Otherwise try something like Abyss which doesn't need a config file.

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written by colindaven colindaven

ls *.fastq is not a good idea, it's better to use shell globs directly (for i in *.fastq). Also, why do a loop when you can:

ls *.fastq | parallel -I fastq_file soapdenovo2 <parameters> fastq_file
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written by Ram Ram

I’m not too familiar with SOAP, so I might be wrong, but as these are paired end reads, presumably there will need to be a step to pair up the R1 and R2 files before passing them to whatever syntax SOAP expects - i.e. before your loop.

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written by Joe Joe

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