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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").

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