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Old 04-25-2017, 12:54 PM   #6
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695
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Considering the cigar strings from alignment, "Match Rate" is the number of symbols indicating a reference match (=) and error rate is the number indicating substitution, insertion, or deletion (X, I, D).

BBMap does not have a PDF, but its documentation is included in /bbmap/docs/guides/BBMapGuide.txt
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