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Aligners

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Copies of presentations from the 1000 genomes group on different sequence aligners.

Presentation from Heng Li (hl3@sanger.ac.uk). In addition Heng says "In addition, I have implemented a new aligner, bwa. It may be of some interest to you. That page also provides a small benchmark to show that bwa works (on simulated data)."

  • MrFAST

Presentation from Can Alkan (calkan@u.washington.edu). Comments: "...the benchmark is quite old. Since then MAQ got a little faster (so did mrFAST). The sequences came from John Stam's lab; so it is ENCODE data; however the sequence quality was low, that was the reason of missing more than half of the reads."

Presentation from Michael Stromberg.

Others (not comprehensive)

  • Bowtie

see Bowtie at sourceforge

  • bwa

see bwa at sourceforge

  • SeqMap

see [http://biogibbs.stanford.edu/~jiangh/SeqMap/ SeqMap)

  • GEM

See GEM at sourceforge

  • novoalign

see novoalign

  • others

see Wikipedia article