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Old 07-18-2014, 08:00 PM   #21
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

I just released a new version of BBTools, 33.11. BBDuk received a slight upgrade, and now has a much-needed additional flag, 'outsingle' (or 'outs'). This is the output stream for reads that pass filtering requirements, but their mate does not. It's most relevant if you set "minlen=X" for quality-trimming, when one read gets trimmed to be shorter than X and the other read is longer than X. It also captures reads such that one had a kmer match to an artifact and the other didn't, or one was adapter-trimmed to be shorter than minlen and the other wasn't, but those cases are probably less interesting.
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