|Bracing against the wind|
Thursday, August 16, 2012
As an experiment, we compared the results to Mosaik. Mosaik can, in some ways, be used to model "truth" for alignment algorithms since it's a fast smith waterman "complete" aligner.
Mosaik, when aligning to the whole genome, found that only 1% of our reads were off target, and none (zero) were off-chromosome.
That's a pretty scary result, except that we knew that there were paralogs out there, and expected some ambiguity, so this exacerbated bwa's issues.
The only other aligner we tested that performed "correctly" on that data set was bwasw, and we had to write our own "paired-end mismatch discarder" because it doesn't handle paired end reads. It's remarkably accurate though.
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