Forum: Bioinformatics
05-11-2009, 07:40 PM
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Replies: 22
Views: 33,387
ISAS Benchmarks Posted
Yes, looks like here we go again. I really can't afford to spend too much time, but I'll answer this one more time as simply as I can put it:
If the run mode is L/M, then for every sequence in the...
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Forum: Bioinformatics
05-11-2009, 10:51 AM
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Replies: 22
Views: 33,387
We recently posted some common benchmarks for...
We recently posted some common benchmarks for ISAS with the new Imagenix Genome Cruncher computer, side by side with a Dell server. The Genome Cruncher runs ISAS between 2 and 3 times faster. You can...
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Forum: SOLiD
04-21-2009, 10:27 PM
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Replies: 24
Views: 8,030
Our output is the same as ABI's alignment...
Our output is the same as ABI's alignment software - so we don't have to worry about "is it too sensitive" or "not sensitive enough". We let ABI scientists spend years (and millions of their R&D...
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Forum: General
04-14-2009, 09:59 AM
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Replies: 5
Views: 7,245
masking reference
I would not recommend masking the reference, as it is just one more step that loses information (as if we don't have enough already, with sequencing errors, and imperfect references). Especially...
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Forum: Bioinformatics
04-14-2009, 09:48 AM
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Replies: 4
Views: 2,992
Fastest Alignment
If you want to do alignment of human genome in minutes instead of hours, you can use ISAS. You will need 16GB for Illumina or 24GB for SOLiD.
What kind of computer do you have ?
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Forum: Bioinformatics
04-08-2009, 02:46 PM
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Replies: 4
Views: 2,750
Dorota,
That is funny, because we get more...
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,...
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Forum: Bioinformatics
04-02-2009, 09:55 AM
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Replies: 22
Views: 33,387
Hi snetmcom,
Sorry if I appear "pretentious...
Hi snetmcom,
Sorry if I appear "pretentious and condescending" to you. I'm just trying to state the facts (and stimulate everyone else to state the facts on their end). I know a lot of people are...
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Forum: Bioinformatics
03-28-2009, 09:01 AM
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Replies: 22
Views: 33,387
Hi Andris,
Sorry for not logging in here for...
Hi Andris,
Sorry for not logging in here for a while... we've been overloaded recently. Every customer tells their friends, and so forth... We're moving into larger offices, so I hope we'll be...
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Forum: Bioinformatics
03-23-2009, 11:22 AM
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Replies: 22
Views: 33,387
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Forum: Bioinformatics
03-12-2009, 06:36 PM
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Replies: 22
Views: 33,387
The time was "real time" (some people call it...
The time was "real time" (some people call it "wall clock time"), and it was on our old 2.0GHz dual socket quad core machine, in other words 8 cores.
Its about 80 to 85 percent of that time for a...
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Forum: SOLiD
03-11-2009, 08:49 AM
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Replies: 24
Views: 8,030
Your free software is wonderful, an amazing...
Your free software is wonderful, an amazing piece of work.... but
I'm still asking my naive question:
How many hours for 100million 25mers in COLORSPACE for 2 mismatches on one computer and 3G...
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Forum: SOLiD
03-10-2009, 11:07 PM
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Replies: 24
Views: 8,030
Those are good questions.
We had to add some...
Those are good questions.
We had to add some special algorithms for SOLiD:
We allow higher mismatches towards the end of the sequence, since SOLiD
get quite noisy towards the end, and our speed...
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Forum: SOLiD
03-10-2009, 10:20 PM
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Replies: 24
Views: 8,030
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Forum: Bioinformatics
03-10-2009, 10:10 PM
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Replies: 3
Views: 4,714
When I enter your sequence in ISAS I get 23...
When I enter your sequence in ISAS I get 23 perfect matches. Below is a transcript of an interactive session.
========================================================
Enter next command, or type...
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Forum: SOLiD
03-10-2009, 08:59 PM
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Replies: 24
Views: 8,030
If your time is precious, try ISAS. Native...
If your time is precious, try ISAS. Native colorspace and as far as we know its the fastest - if I'm wrong and there is a faster solution please enlighten me !
100 million 25mers on one computer...
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Forum: SOLiD
03-10-2009, 08:41 PM
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Replies: 22
Views: 43,532
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Forum: Events / Conferences
03-10-2009, 08:35 PM
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Replies: 23
Views: 9,952
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Forum: Bioinformatics
03-09-2009, 05:08 PM
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Replies: 22
Views: 33,387
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Forum: Bioinformatics
03-09-2009, 05:01 PM
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Replies: 9
Views: 3,313
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Forum: Bioinformatics
03-06-2009, 10:14 PM
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Replies: 22
Views: 33,387
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Forum: Bioinformatics
03-06-2009, 03:41 PM
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Replies: 22
Views: 33,387
Hi Klaus,
We search for any "mutations"...
Hi Klaus,
We search for any "mutations" which have up to the maximum specified mismatches. In the case of the public data which I just ran, the spec was "maximum 2 substitutions". It doesn't...
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Forum: Bioinformatics
03-06-2009, 03:12 PM
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Replies: 22
Views: 33,387
Thanks for the link Ih3,
I was worried that...
Thanks for the link Ih3,
I was worried that it would take forever to download, but actualy those files are quite small, only 12M 50mers, and they downloaded rather quickly. I ran each file...
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Forum: Bioinformatics
03-05-2009, 03:02 PM
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Replies: 22
Views: 33,387
How to get SOLiD data for alignment
As for the ABI data, its all downloadable from their web site,
although it takes forever, and its a pain to find the link. If you can't find the link, I'll search for it. As for the finite bandwidth...
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Forum: SOLiD
03-05-2009, 02:57 PM
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Replies: 8
Views: 3,043
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Forum: Bioinformatics
03-05-2009, 01:46 PM
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Replies: 22
Views: 33,387
ISAS Alignment Software
Hi,
We're from a company called Imagenix Technologies.
We just want to give everyone a "heads up". We'll be at the NextGen Sequencing conference in San Diego in 2 weeks, doing real-time live...
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