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Old 04-14-2011, 09:33 AM   #4
Location: Boston, MA

Join Date: Nov 2009
Posts: 12

BWT-based mappers are theoretically fastest ones up until certain read length (don't remember exactly, but something like 400-1000 bp). There is a bunch of papers out there describing this.

Bowtie is extremely fast but it is arguable whether it is the best one since the definition of "best" depends on your application. For example, Bowtie is one of the best ones for RNA-seq, but no so much for resequencing, targeted sequencing, and whole-genome sequencing, where many people prefer BWA.
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