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== Read mappers that we like are ==
[[Karma]] - Currently under development here in Michigan; trades memory for speed, but is both fast and sensitive (now matches or exceeds both bwa and NovoAlign), and highly effective on nodes with high core counts.
All of these should output [[SAM]] format.
== Other Aligners ==
[http://maq.sourceforge.net/ MAQ] - The venerable short read aligner developed by Richard Durbin and Heng Li.