Given short reads and reference, I wonder is there a way or tool can quickly find out which reads are x-distance (x can be 0,1,2,...hamming distance from the reference) aligned to the reference?
Thank you.
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written
by
chongchu.cs •
1 answer
I think Bowtie1 can do that, up to a hamming distance of 3. I'm not certain whether Bowtie1 guarantees finding all possible sites for hamming distance 0-3, but it might.
BBMap can do that fairly accurately for a pretty high hamming distance (perhaps 10% of the read length), if you use the flag strictmaxindel=0. But, it will not guarantee correctness in cases where a read maps better with an indel than with tons of substitutions; instead, it will map the read with an indel and then discard it because it fails your filter of having indels.
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written
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Brian Bushnell
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