Hello,
I'm using BBduk to trim adapter sequences from my reads. From the help manual I see the editdistance and hammingdistance options, but they set a fixed number of mismatches, independent of the length of the match. Is it possible to specify an error rate (like 10%) that allows errors in the match depending on the length of the match?
This feature is available in cutadapt, but I'd rather do it with bbduk if possible to shorten my pipeline.
I'm using BBduk to trim adapter sequences from my reads. From the help manual I see the editdistance and hammingdistance options, but they set a fixed number of mismatches, independent of the length of the match. Is it possible to specify an error rate (like 10%) that allows errors in the match depending on the length of the match?
This feature is available in cutadapt, but I'd rather do it with bbduk if possible to shorten my pipeline.
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