Read Mapping: Difference between revisions
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== Read mappers that we like are == | == 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. | ||
[ | [http://bio-bwa.sourceforge.net BWA] - A fast aligner developed by Richard Durbin and Heng Li. | ||
[http://www.novocraft.com NovoAlign] - Potentially, a much more sensitive, but slow, aligner. | [http://www.novocraft.com NovoAlign] - Potentially, a much more sensitive, but slow, aligner. | ||
Revision as of 09:41, 26 March 2010
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.
