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Old 09-30-2015, 07:52 PM   #41
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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It is almost possible to do this with Seal, which outputs reads into bins based on kmer matching.

seal.sh in=reads.fq pattern=%.fq k=6 restrictleft=6 mm=f ref=barcodes.fa rcomp=f

That would require a file "barcodes.fa" like this:
>AACTGA
AACTGA
>GGCCTT
GGCCTT

etc., with one fasta entry per barcode, so the output reads would be in file AACTGA.fq and so forth. This is sort of a common request, so maybe I will make it unnecessary to provide a fasta file of the barcodes. Does that matter to you either way?

However, BBDuk has the flags "skipr1" and "skipr2", which allow it to only do kmer operations on one read or the other. Seal currently lacks this, but it's essential for processing inline barcodes. I'll add it for the next release.
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