Question: How to perform SOAPdenovo for many samples
0
gravatar for michaelijesse
4 months ago by
michaelijesse0 wrote:

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 • 241 views
ADD COMMENTlink modified 4 months ago by h.mon24k • written 4 months ago by michaelijesse0

Why is this a blog type post? Please read: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking

ADD REPLYlink written 4 months ago by RamRS20k

Tried anything like looping, GNU parallel or the like?

ADD REPLYlink written 4 months ago by ATpoint14k

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

ADD REPLYlink written 4 months ago by h.mon24k

try to follow soapdenovo2 manual here: https://hcc-docs.unl.edu/display/HCCDOC/SOAPdenovo2. For paired end, you can create one single config file and submit it to cluster. Example script is furnished in the manual.

ADD REPLYlink written 4 months ago by cpad011211k
0
gravatar for colindaven
4 months ago by
colindaven1.1k
Hannover Medical School
colindaven1.1k wrote:
#!/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.

ADD COMMENTlink modified 4 months ago • written 4 months ago by colindaven1.1k
1

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
ADD REPLYlink written 4 months ago by RamRS20k

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.

ADD REPLYlink written 4 months ago by jrj.healey11k
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