Read Mapping: Difference between revisions
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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. | [[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. | ||
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All of these should output [[SAM]] format. | All of these should output [[SAM]] format. | ||
== Other Aligners == | == Other Aligners == | ||
[http://maq.sourceforge.net/ MAQ] - The venerable short read aligner developed by Richard Durbin and Heng Li. | [http://maq.sourceforge.net/ MAQ] - The venerable short read aligner developed by Richard Durbin and Heng Li. | ||
Latest revision as of 22:53, 17 November 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.
