Read Mapping
From Genome Analysis Wiki
Jump to navigationJump to searchRead 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.
