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Old 07-21-2016, 05:09 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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I suggest you try BBMap, which is quite tolerant of low identity; it typically allows mapping down to around 60-70% identity. For very high sensitivity, try this command:

Code:
bbmap.sh in=reads.fq out=mapped.sam vslow minid=0.6 maxindel=5 k=11
Using only the first 17 bp of sequences will hurt the ability to map with BBMap, though; you need to use the full sequences.
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