Aligner that reports all alignments?

[Rocketknight]

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.

[mchaisso]

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.

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.

[Rocketknight]

Good point. I'm interested in 454/Ion Torrent or PacBio reads, so thanks for the info! I didn't realize mrfast could handle Ion Torrent reads, they're pretty specific about calling it an Illumina read aligner on their site. I'll give it a try though!

[suryasaha]

Have you tried using other aligners with parameters optimized for returning all hits like bowtie2 (-a), bwa mem (-a), novoalign (-r All) and tmap (mapall)? Thanks

[GenoMax]

See Heng Li's announcement about BWA-MEM. http://www.biostars.org/p/67236/

[Rocketknight]

Oh god, I'm sorry. I kept looking through that manual and never saw that. Sorry!

[suryasaha]

Glad it helped :-)