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Originally posted by hannat View PostBowtie -n mode, allow n(0-3) mismatch in first L(28bp) base seed, what about the rest of the reads beside the seed, how can i increase the mismatch?
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SeqMap allows up to 5 mismatches/deletions
But it is slower than the other aligners if you want to take advantage of this feature.
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Novoalign is able to handle this task with Illumina and SOLiD reads. The aligner can be downloaded for free at www.novocraft.com
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There have been lots of comments on how to use other programs or parameter sets to get around this, but I thought I'd comment on why some programs limit to 3 mismatches.
The Burrows-Wheeler algorithm (used by bowtie and BWA) is really fast, but doesn't handle mismatches very well. There are at least two workarounds used, one is the seed-extend method (so it only really has to handle mismatches in the seed) and the other is a backtracking heuristic. The backtracking heuristic isn't robust enough to work for more than 3 mismatches without losing all of the speed gains for using Burrows-Wheeler.
Other programs use different algorithms, which will be slower for fewer mismatches, but able to handle 4+ mismatches without losing lots of speed or taking up tons more memory. That's why it's useful to switch to a program that doesn't map using Burrows-Wheeler when you want a large amount of mismatch tolerance within the first 20-30 nucleotides.
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You can try batman-aligner, it allows you to map up to 15-mismatches in the whole read.
Although based on my experience, if you allow more than 8 mismatch in the alignment, usually the non-bwt-based tools (maq,rmap) will be faster.
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