Difference between revisions of "Read Mapping"

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(clean up karma comments)
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== Read mappers that we like are ==
 
== Read mappers that we like are ==
  
[http://bio-bwa.sourceforge.net BWA] - A much faster aligner developed by Richard Durbin and Heng Li.
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[[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; a memory hog, but fast and sensitive.
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[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.