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== Read mappers that we like are ==
[http://bio-bwa.sourceforge.net BWA] - A much faster aligner developed by Richard Durbin and Heng Li.
[[Karma]] - Currently under development here in Michigan; a memory hog, but fast and sensitive.
[http://www.novocraft.com NovoAlign] - Potentially, a much more sensitive, but slow, aligner.
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.
[http://bio-bwa.sourceforge.net BWA] - A much faster aligner developed by Richard Durbin and Heng Li.
[[Karma]] - Currently under development here in Michigan; a memory hog, but fast and sensitive.
[http://www.novocraft.com NovoAlign] - Potentially, a much more sensitive, but slow, aligner.
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.
