Thread: BFAST published
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Old 11-20-2009, 02:09 AM   #8
NGSfan
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Location: Austria

Join Date: Apr 2009
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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.
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