Difference between revisions of "Read Mapping"
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== Read mappers that we like are == | == Read mappers that we like are == | ||
| − | [http://bio-bwa.sourceforge.net BWA] - A | + | [[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. | ||
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.
