Question: Is it possible to use interleaved fastq data with SOAPdenovo?
0
gravatar for Daniel Standage
4.3 years ago by
Daniel Standage3.9k
Davis, California, USA
Daniel Standage3.9k wrote:

I am assembling an insect genome with SOAPdenovo and have my data in interleaved Fastq format. I can convert the interleaved files to paired files easily enough if I need to, but it's a big time/space inconvenience. Is it possible to run SOAPdenovo on interleaved Fastq files?

soapdenovo fastq assembly • 1.3k views
ADD COMMENTlink modified 4.3 years ago by Renesh1.6k • written 4.3 years ago by Daniel Standage3.9k
0
gravatar for Renesh
4.3 years ago by
Renesh1.6k
United States
Renesh1.6k wrote:

I never tried this before, but in documentation it is provided,

#a single fasta file for paired reads
p=/path/**LIBNAMEA**/pairs1_in_one_file.fa

SeeĀ http://soap.genomics.org.cn/soapdenovo.html#comm2

ADD COMMENTlink written 4.3 years ago by Renesh1.6k

Indeed. I saw that option and tried it, but this led to issues with SOAPdenovo's read parser (I killed the process when it was trying to load the 530 billionth read--my data set didn't have nearly that many reads). The p option therefore appears to be fasta-specific. :(

ADD REPLYlink written 4.3 years ago by Daniel Standage3.9k

yes, the p option is fasta specific. You can convert fastq into fasta and run SOAPdenovo. Hope that works.

ADD REPLYlink written 4.3 years ago by Renesh1.6k

Heh. The whole purpose of this question is to avoid file conversion...

ADD REPLYlink written 4.3 years ago by Daniel Standage3.9k

I mean to say instead of converting separate paired files, you have to convert into single fasta file only. As the fasta file will not contain quality values you can reduce the space unless you don't need quality values in separate files.

ADD REPLYlink written 4.3 years ago by Renesh1.6k
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