Thread: BFAST published
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Old 11-11-2009, 12:30 PM   #6
Nils Homer
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Location: Boston, MA, USA

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Originally Posted by dawe View Post
I've downloaded it and if it runs as stated in the paper I'm ready to use it especially for resequencing and SNP projects. I'm a bit worried about speed (and memory usage) but, as said, if the error rate is so low...
SAM output is a great feature, I'm running almost aligner-independent now :-)
The current version allows the user to get rid of the memory problem at the cost of some speed. You use the "-d" option to split the index during index creation. This allows you to run BFAST in 4GB environments etc.

@dawe and @lh3
The assumption that the error rate is below 6% is not valid for ABI SOLiD data. With BFAST's ability to be very sensitive, we regularly observe runs with >10% (color/raw) error rates towards the ends of reads, even though after alignment the base error rate is well below 1% (kudos to 2-base encoding).
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