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Forum: Bioinformatics 05-11-2009, 07:40 PM
Replies: 22
Views: 31,885
Posted By BioWizard
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...
Forum: Bioinformatics 05-11-2009, 10:51 AM
Replies: 22
Views: 31,885
Posted By BioWizard
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...
Forum: SOLiD 04-21-2009, 10:27 PM
Replies: 24
Views: 6,796
Posted By BioWizard
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...
Forum: General 04-14-2009, 09:59 AM
Replies: 5
Views: 5,907
Posted By BioWizard
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...
Forum: Bioinformatics 04-14-2009, 09:48 AM
Replies: 4
Views: 2,477
Posted By BioWizard
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 ?
Forum: Bioinformatics 04-08-2009, 02:46 PM
Replies: 4
Views: 2,309
Posted By BioWizard
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,...
Forum: Bioinformatics 04-02-2009, 09:55 AM
Replies: 22
Views: 31,885
Posted By BioWizard
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...
Forum: Bioinformatics 03-28-2009, 09:01 AM
Replies: 22
Views: 31,885
Posted By BioWizard
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...
Forum: Bioinformatics 03-23-2009, 11:22 AM
Replies: 22
Views: 31,885
Posted By BioWizard
Thanks to all the people that visited our booth...

Thanks to all the people that visited our booth in the San Diego Next Gen Sequencing Conference.

I also want to thank Hadar and Ryan who performed alignments in real time for the customers, day...
Forum: Bioinformatics 03-12-2009, 06:36 PM
Replies: 22
Views: 31,885
Posted By BioWizard
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...
Forum: SOLiD 03-11-2009, 08:49 AM
Replies: 24
Views: 6,796
Posted By BioWizard
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...
Forum: SOLiD 03-10-2009, 11:07 PM
Replies: 24
Views: 6,796
Posted By BioWizard
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...
Forum: SOLiD 03-10-2009, 10:20 PM
Replies: 24
Views: 6,796
Posted By BioWizard
"should be fast" but takes anywhere from 6 to 66...

"should be fast" but takes anywhere from 6 to 66 hours on the other alignment systems.
So many people say "our aligner is fast" but its tough to get numbers....
The ones that used to post numbers...
Forum: Bioinformatics 03-10-2009, 10:10 PM
Replies: 3
Views: 3,954
Posted By BioWizard
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...
Forum: SOLiD 03-10-2009, 08:59 PM
Replies: 24
Views: 6,796
Posted By BioWizard
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...
Forum: SOLiD 03-10-2009, 08:41 PM
Replies: 22
Views: 42,302
Posted By BioWizard
ISAS (color space version) works natively in...

ISAS (color space version) works natively in colorspace, and even "Valid Adjacent". See the thread about ISAS for explanation.
Forum: Events / Conferences 03-10-2009, 08:35 PM
Replies: 23
Views: 8,087
Posted By BioWizard
Yes, doxologist, there is "something for...

Yes, doxologist, there is "something for everyone".
Forum: Bioinformatics 03-09-2009, 05:08 PM
Replies: 22
Views: 31,885
Posted By BioWizard
There have been many downloads of that 1.3GB file...

There have been many downloads of that 1.3GB file in the last 3 days, but so far as I know... no one has volunteered to host this file for the community - where's big government when you need them :)...
Forum: Bioinformatics 03-09-2009, 05:01 PM
Replies: 9
Views: 2,733
Posted By BioWizard
If you're looking for the fastest colorspace...

If you're looking for the fastest colorspace alignemnt,
check out the thread:

"Alignment Software breaks speed records "
Forum: Bioinformatics 03-06-2009, 10:14 PM
Replies: 22
Views: 31,885
Posted By BioWizard
OK, the file (1300MB) has been uploaded. Anyone...

OK, the file (1300MB) has been uploaded.
Anyone with big space/bandwidth that can copy it from
www.imagenix.com/publicdata
and put on your site, tell me so I can remove it.
Forum: Bioinformatics 03-06-2009, 03:41 PM
Replies: 22
Views: 31,885
Posted By BioWizard
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...
Forum: Bioinformatics 03-06-2009, 03:12 PM
Replies: 22
Views: 31,885
Posted By BioWizard
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...
Forum: Bioinformatics 03-05-2009, 03:02 PM
Replies: 22
Views: 31,885
Posted By BioWizard
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...
Forum: SOLiD 03-05-2009, 02:57 PM
Replies: 8
Views: 2,663
Posted By BioWizard
OK - noted ! I moved the discussion to a new...

OK - noted !

I moved the discussion to a new thread in the BioInformatics forum.
Forum: Bioinformatics 03-05-2009, 01:46 PM
Replies: 22
Views: 31,885
Posted By BioWizard
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...
Showing results 1 to 25 of 27

 


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