Read Mapping

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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.

BWA - A fast aligner developed by Richard Durbin and Heng Li.

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.