Difference between revisions of "Read Mapping"

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>== Read mappers that we like are ==
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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.
 
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=[http://ekydewequ.co.cc UNDER COSTRUCTION, PLEASE SEE THIS POST IN RESERVE COPY]=
 
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=[http://ekydewequ.co.cc CLICK HERE]=
 
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== 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 21:53, 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.