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Old 07-24-2014, 09:39 AM   #6
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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Sham,

You might try BBMap, which is quite sensitive and supports short seeds (value of 'k'). By default k=13 and it gets exponentially slower (with higher sensitivity) as you reduce it, but it should still be fast enough for only 3m short sequences. If 9 is not sensitive enough you can try reducing it as low as 7, perhaps. The command would be something like this:

bbmap.sh -Xmx23g in=reads.fq ref=hg19.fa k=9 maxindel=4 slow out=mapped.sam ambig=all
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