NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.
Copies of presentations from the 1000 genomes group on different sequence aligners.
Presentation from Heng Li (firstname.lastname@example.org). 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)."
Presentation from Can Alkan (email@example.com). 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)
see [http://biogibbs.stanford.edu/~jiangh/SeqMap/ SeqMap)