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Forum: Bioinformatics 10-30-2011, 07:04 PM
Replies: 1
Views: 3,035
Posted By geschickten
Computational Biology / Bioinformatics companies

Like the "Software packages for NGS data analysis" thread I guess a list of companies who offer exclusive data analysis products/services will be of great help too.

In India

1. Geschickten...
Forum: Introductions 10-30-2011, 06:51 AM
Replies: 0
Views: 2,029
Posted By geschickten
iOmics - Cloud based NGS data analysis platform

Hello All,

About Geschickten

Geschickten Biosciences a Life Sciences and Healthcare technology company focusing on integrating Genomic, Genetic, Medical and Clinical information to faster and...
Forum: Bioinformatics 07-25-2010, 11:17 PM
Replies: 6
Views: 3,949
Posted By geschickten
Hi BioSlayer... hopefully by now you must have...

Hi BioSlayer... hopefully by now you must have compiled the list. Can you please share it with other users...
Forum: Bioinformatics 07-25-2010, 11:06 PM
Replies: 12
Views: 3,520
Posted By geschickten
Hi Janina, do you have gsMapper or any other...

Hi Janina, do you have gsMapper or any other similar s/w? if not write to me; I can probably help you...
Forum: Bioinformatics 07-25-2010, 11:02 PM
Replies: 10
Views: 2,226
Posted By geschickten
Hi All, We have a MAQ that works with 125bp...

Hi All,

We have a MAQ that works with 125bp Illumina read and we also a version that works with 454 data. Its not in open domain. If anybody is interested then please send me a request at...
Forum: Bioinformatics 07-22-2010, 06:24 AM
Replies: 17
Views: 3,378
Posted By geschickten
Sure; please email your queries to...

Sure; please email your queries to santhosh.gandham@geschickten.com. He will help you... thanks for using the software....
Forum: Bioinformatics 07-22-2010, 02:36 AM
Replies: 17
Views: 3,378
Posted By geschickten
Ms@New - It works with MAQ 0.6.8; the source is...

Ms@New - It works with MAQ 0.6.8; the source is not available; but I can send you the executable. CloudMAQ is a wrapper around MAQ and we have not modified the original MAQ; hence the results of...
Forum: Bioinformatics 01-12-2010, 06:20 PM
Replies: 17
Views: 3,378
Posted By geschickten
We are not distributing MAQ; you have to download...

We are not distributing MAQ; you have to download it from sourceforge. The README in the distribution has all the details. Thanks

-p
Forum: Bioinformatics 01-12-2010, 05:55 PM
Replies: 17
Views: 3,378
Posted By geschickten
nilshomer & Jonathan I know its a pain to...

nilshomer & Jonathan

I know its a pain to pen a few details before you download any softwareand I am sorry for that; well Jonathan you are partially right; I mean what we have is a wrapper and we...
Forum: Bioinformatics 01-11-2010, 11:09 PM
Replies: 1
Views: 2,176
Posted By geschickten
List of Assembly and Analysis tools

Hi All,

We are determined to parallelize and Cloud enable a lot of Assembly and Analysis software. In this regard I request all the members to list the most wanted assembly and analysis software...
Forum: Bioinformatics 01-11-2010, 10:36 PM
Replies: 11
Views: 5,536
Posted By geschickten
Well all I can say is if you want to use MAQ on...

Well all I can say is if you want to use MAQ on many cores or on a cluster ( built using commodity machines) then please try our version at http://www.geschickten.com/PaCGeE.html

Your suggestions...
Forum: Bioinformatics 01-11-2010, 10:32 PM
Replies: 17
Views: 3,378
Posted By geschickten
I am pleased to announce that Cloud-MAQ is...

I am pleased to announce that Cloud-MAQ is available for download. For enthusiasts please go to http://www.geschickten.com/PaCGeE.html.

Please remember that your suggestions and feedback are...
Forum: Bioinformatics 12-22-2009, 07:13 AM
Replies: 6
Views: 5,184
Posted By geschickten
Hi MicroOmicsMan, Well you may not need to...

Hi MicroOmicsMan,

Well you may not need to know programming or scripting to use any tools; but NGS data analysis according to me is more computational than biology and hence it always helps if you...
Forum: Bioinformatics 12-22-2009, 03:52 AM
Replies: 17
Views: 3,378
Posted By geschickten
We will post the link on our website soon after...

We will post the link on our website soon after holidays. Thank you and Happy Holidays to you all....
Forum: Bioinformatics 12-16-2009, 09:26 PM
Replies: 17
Views: 3,378
Posted By geschickten
I will post the link soon. We are in the last leg...

I will post the link soon. We are in the last leg of quality testing...thank you
Forum: Bioinformatics 12-13-2009, 08:30 PM
Replies: 17
Views: 3,378
Posted By geschickten
Cloud-MAQ

We have developed an enhanced version of MAQ called Cloud-MAQ. It outperforms MAQ in terms of runtime. For 120 million (33 base, Illumina) sequence reads on a single core, MAQ took 8hrs for reference...
Forum: Bioinformatics 10-26-2009, 05:58 AM
Replies: 10
Views: 3,708
Posted By geschickten
Hi jasonbcold, I guess it's nothing to do...

Hi jasonbcold,

I guess it's nothing to do with H/w; if you see the pthreads part of the BWA code you will understand.. I still have to dive deep into the code but at a high level I can guess the...
Forum: Bioinformatics 10-22-2009, 08:13 PM
Replies: 10
Views: 3,708
Posted By geschickten
jasonbcold, Well this is a common thing I...

jasonbcold,

Well this is a common thing I hear from many people doing analysis work on multi CPU/core machines. Well according me if the software is parallelized/optimized for shared/distributed...
Forum: Bioinformatics 10-08-2009, 02:48 AM
Replies: 5
Views: 2,496
Posted By geschickten
Parallel Bioinformatics tools

Can we list all the available ( open source and commercial) parallel (written using MPI / Map Reduce etc) bioinformatics tools. It can include tools that cover both secondary and tertiary analysis...
Forum: Bioinformatics 10-07-2009, 11:05 AM
Replies: 27
Views: 10,668
Posted By geschickten
Jnfass, You say that you have done Velvet...

Jnfass,

You say that you have done Velvet assemblies with > 100M reads (some paired-end) on a 512G machine; we know that Velvet is not a parallel assembler and you say that the Sun box ( I assume...
Forum: Bioinformatics 10-05-2009, 10:06 AM
Replies: 27
Views: 10,668
Posted By geschickten
Hi Zigster, Can you please share the exact...

Hi Zigster,

Can you please share the exact configuration of the machine that you used to for this run. Also what's your take on if somebody allows you to run this in Cloud?? would you go for it?
Forum: Bioinformatics 10-05-2009, 10:02 AM
Replies: 27
Views: 10,668
Posted By geschickten
Hi jnfass, Can you please share some...

Hi jnfass,

Can you please share some information on who's doing the work on parallelizing assemblers? Also kindly point to some good open source parallel assemblers if you know any.. thank you
Forum: Service Providers 08-25-2009, 01:53 AM
Replies: 162
Views: 155,226
Posted By geschickten
A stat up called "Geschickten Solutions" in the...

A stat up called "Geschickten Solutions" in the area of Computational Biology and High Performance Computing from India is poised to become a one stop shop for all OMIC activities. They are the...
Forum: Bioinformatics 08-20-2009, 08:58 AM
Replies: 2
Views: 1,245
Posted By geschickten
genome assembler on cDNA data

Why can't we use with genome assemblers for assembly of cDNA?
Forum: Bioinformatics 08-14-2009, 12:37 AM
Replies: 27
Views: 10,668
Posted By geschickten
NST, do you think you can share this papaer "De...

NST, do you think you can share this papaer "De novo Transcriptome Assembly with Abyss, Birol et al"

-p
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