Dan Koboldt of the MassGenomics blog will be presenting a poster at this year's Marco Island sequencing meeting evaluating short read aligners. He's compiled a partial list of aligners, which include first and foremost, Maq. "It’s safe to say that we decided to gamble on Maq over a year ago, and so far, the bet has paid off," he writes. Other options include Novoalign, Bowtie, cross_match, RMAP (which he hears the developers have stopped working on), and SOAP ("probably a tool to watch"). While his evaluations seem to beg for aligners that can handle gaps and paired end reads, his main criteria are speed, compatibility with in-house platforms, and "aligners that can beat Maq -- in performance, features, or sensitivity -- and that's not easy to do. Maq is fast and does quality-based alignment, single or paired-end, assembly, SNP calling… there's a reason why the rest of the industry seems to be conforming to it," he writes.
Maq Still Leading the Way
Jan 22, 2009