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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 Post -
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!Comment
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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)? ThanksComment
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Oh god, I'm sorry. I kept looking through that manual and never saw that. Sorry!Comment
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Glad it helped :-)Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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