Question: How to perform SOAPdenovo for many samples
0
gravatar for michaelijesse
12 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 • 594 views
ADD COMMENTlink modified 12 months ago by h.mon28k • written 12 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 12 months ago by RamRS24k

Tried anything like looping, GNU parallel or the like?

ADD REPLYlink written 12 months ago by ATpoint26k

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 12 months ago by h.mon28k

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 12 months ago by cpad011212k
0
gravatar for colindaven
12 months ago by
colindaven1.8k
Hannover Medical School
colindaven1.8k 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 12 months ago • written 12 months ago by colindaven1.8k
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 12 months ago by RamRS24k

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 12 months ago by Joe15k
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