Hi, I'm looking for an aligner that reports multiple/all hits rather than just a single one. I know mrfast or BWA-short can do this for Illumina data, but is there any aligner that can do this that works on non-Illumina reads? My searches haven't turned up anything.
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What type of non-Illumina reads? There are now a few categories out there. mrFAST should work for Ion Torrent. If you are using pacbio, the blasr parameter -bestn limits the number of hits you will get, up to 2^32 - 1.
Originally posted by Rocketknight View PostHi, I'm looking for an aligner that reports multiple/all hits rather than just a single one. I know mrfast or BWA-short can do this for Illumina data, but is there any aligner that can do this that works on non-Illumina reads? My searches haven't turned up anything.
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