Thread: BFAST published
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Old 11-20-2009, 11:40 AM   #11
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
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Originally Posted by NGSfan View Post
Congratulations Nils Homer!

I really enjoyed your paper - I also must thank you for the in-depth supplement that really explained the history behind BFAST and other aligners. It shows you put a lot of thought into this.

My only question in regards to BFAST performance, is if you have recently compared it to SSAHA2 ? I know you did not intend to be comprehensive in this paper when comparing algorithms (it is impossible to be comprehensive now with 30+ aligners available), but I feel that SSAHA2 might be a real benchmark to compare against for speed and accuracy. Would you say that BFAST would run faster than SSAHA2 given similar accuracy settings?

Thanks for releasing your software. I will be trying it now.
I have not tested SSAHA2 lately, although I think SSAHA2 is built for longer reads if I am correct. Also note that since the release of the paper, BFAST's speed has improved by an order of magnitude (submitted as another paper).
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