Comments (6)
I'll chime in on what it currently does (though I am not sure I agree with it).
To start the alignment, the kmer profiling treats N's like its own base. So, kmers with N's in them are considered, however, there needs to be an exact string match between the two reads (N's included) to initiate the overlap.
N's are currently treated on par with the other bases. So if a 'N' mismatches with a 'A' the algorithm will take the highest q score still (hopefully it is the A). Additionally, it will subtract the qscores just as if N was normal base.
@msettles What are your thoughts?
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Any movement on this? Can it be closed?
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I'm not sure, going to have to let David comment.
I think we did end up having one difference from your version of the approach above. For matching bases, I think we are adding q-scores with a ceiling of 40. This improves qualities for low-quality ends that overlap and match.
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2+ years later going to go ahead and close
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