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Old 05-20-2014, 08:26 PM   #5
Brian Bushnell
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Location: Walnut Creek, CA

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

Yes, you can quality-trim and adapter-trim at the same time with BBDuk. The command line would be like this:

bbduk.sh -Xmx1g in1=r1.fq in2=r2.fq out1=clean1.fq out2=clean2.fq minlen=25 qtrim=rl trimq=10 ktrim=r k=25 mink=11 ref=truseq.fq.gz hdist=1

You can use whatever adapter sequence you want (with the "ref=" flag), and I include the Illumina truseq adapters with the BBMap package, in the "resources" directory. The command above will allow up to 1 mismatch (hdist=1) and trim as few as 11 trailing adapter bases. You can of course increase the number of mismatches and decrease the minimal number of trailing bases that are trimmed. If you have really low-quality reads with an average insert size close to the read length (and thus a high rate of adapters) you should probably set hdist=2 and mink=6 to remove more of them, but be aware that those settings will increase the false positive detection rate.

It's best to do adapter-trimming first, then quality-trimming, because if you do quality-trimming first, sometimes adapters will be partially trimmed and become too short to be recognized as adapter sequence. When you run BBDuk with both quality-trimming and adapter-trimming in the same run, it will do adapter-trimming first, then quality-trimming.
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