Thread: ISAS software
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Old 04-06-2009, 10:26 AM   #4
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Originally Posted by f85978 View Post
Hi, we have to make a decision what to buy Illumina or Solid3 shortly. We found out from this forum that ISAS software is a very critical tool for alignment using Solid3. We had meeting with AB people and they didn't know anything about the ISAS software. They told us that there are many available software which work fine in color space. Is it true? What should we ask them for before signing our contract?

Thanks, Dorota
It's the guy who works for ISAS who gave you that impression. I don't know that anyone posting has ever used the software (or ever will, given the attitude of the ISAS represenative here).

For seqcap, you'll probably be aligning to regions of not more than 10-20 Mb? Speed is not as crucial an issue as it would be if you were doing, say, a whole mammalian genome, or chip-seq, both of which align to a whole 30 Gb genome.

So don't feel that you need to pay top dollar for the very fastest aligner out there. I'm not as familiar with the available color-space assemblers, but I bet there's something out there that's pretty good, and free.
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