Fast or Accurate?

Mass Genomics’ Dan Koboldt is part of the 1,000 Genomes Pilot 3 and the group is putting together a list of aligners to use. The aligners he suggested, Bowtie, Novoalign, and SHRiMP, were deemed not accurate enough, accurate but slow, and slow, respectively. And Kobolt says this points out “the key issue surrounding short read alignment for variant detection — finding the balance between speed and sensitivity.” “The ultimate short read aligner, in my opinion, would have Bowtie-like speed, Novoalign-like sensitivity, and the widespread community support that Maq enjoys,” he writes.