Is it possible to use interleaved fastq data with SOAPdenovo?

Question

[Daniel Standage]

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?

Answer 1

[Renesh]

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

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

[Daniel Standage]

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. :(

[Renesh]

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

[Daniel Standage]

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

[Renesh]

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.