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Old 08-07-2008, 01:54 PM   #54
apfejes
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Location: Oakland, California

Join Date: Feb 2008
Posts: 236
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Thanks - all I know is that when I spoke to my contact at Bioinformatics Solutions, they were using the core of the software to generate benchmarks, but were still working on the application itself. A lot of my questions weren't answered, unfortunately.

Either way, I agree, once we pass 64bp reads (I've heard we're going to start doing 72bp test runs next week), we're going to leave the realm of short read aligners and need to start dealing with medium length (100-1000bp) read aligners, anyhow. (I'm not sure what's in that space, though: blast, blat, exonerate?)

As an aside, I'll save the term "long read alignments" for when Pacific Biosciences releases their SMRT (single molecule - real time) sequencing machine. 5-25k reads are about as long as I expect are going to be necessary for any application, though at that point, you're probably better off doing assembly than alignments.
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