Read Mapping
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Read mappers that we like are
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. NovoAlign - Potentially, a much more sensitive, but slow, aligner.
All of these should output SAM format.
Other Aligners
MAQ - The venerable short read aligner developed by Richard Durbin and Heng Li.
