RNA-Seq de novo assembly: split ion proton read sequences

Question

[jules.augley]

Hi all,

I am testing different RNA-Seq de novo transcriptome assembly strategies using Ion Proton reads. To test a particular hypothesis, I wish to chop up the reads, in fastq format, so the sequences are smaller, but not discard any sequence data (sequences have already been quality trimmed/cleaned). Essentially I want to reduce the read length and increase the number of reads e.g. if I halve the read length I will double the number of reads.

Is anyone aware of any tools that can do this? I am not sure how to go about giving identifiers to the new 'reads' that will be created by doing this.

Thanks

[jules.augley]

Excellent thank you so much, I shall try it out.

Jules

Answer 1

[Brian Bushnell]

The BBMap package has a program called Shred that should do what you want:

shred.sh in=reads.fq out=shredded.fq length=50 overlap=0 minlength=1

That will generate 50bp reads from the input, using every base exactly once, with no overlap. You can play with the parameters as needed; I think they're pretty straightforward, but let me know if you have any questions. If you run shred.sh with no parameters it will give longer descriptions.

Sourceforge is down right now but you can download it here.