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Old 04-04-2009, 10:49 PM   #1
f85978
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Default ISAS software

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
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Old 04-05-2009, 01:22 AM   #2
Chipper
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Hi,

ISAS is just another aligner (presumably faster than ABs matching pipeline), there are several other free options including BFAST and ZOOM!, and commercial such as those from Genomatix and CLC bio.

What applications will it mainly be used for, and what are your main requirements?
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Old 04-05-2009, 04:52 AM   #3
f85978
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Hi,

We are mainly interested in targeted resequencing.
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Old 04-06-2009, 09:26 AM   #4
swbarnes2
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Quote:
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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Old 04-08-2009, 01:46 PM   #5
BioWizard
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Dorota,

That is funny, because we get more ABI orders for ISAS licenses, even today
Does ABI have sales people in Saudi Arabia ?!
Anyway - tell them to ask their headquarters in Foster City, California
The people who are responsible for SOLiD alignment know ISAS very well

I have to admit, though, that what the two posters above wrote might be relevant for you:
If you're not using whole human reference (3Gbases), but just some small region of
a human, or some small organism (a few Mbases), then you can definitley use one of the slow alignment systems, which are free. If we do it in 5 minutes, and they do it in 50 minutes, the 45 minutes difference might not matter to you. Its when they take a whole day (or, as one customer told us: "weeks"), that you need us.
One thing to consider, maybe, even if using a small targeted area (of human), is that by running with the full human reference, (and later filtering just your region of interest) you get to find out which hits (in your targeted area) are really unique.

Also - looks like many people don't know, because we're famous with SOLiD (few alternatives with color code) but ISAS is ALSO available for Illumina, so you can go either way.

Good luck.
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