Thread: BFAST published
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Old 11-11-2009, 12:30 PM   #6
nilshomer
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Quote:
Originally Posted by dawe View Post
Congratulations!
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 :-)
@dawe
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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