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Search: Posts Made By: Roald
Forum: Bioinformatics 03-28-2011, 11:02 AM
Replies: 65
Views: 33,292
Posted By Roald
Smile Thanks!!

Thanks for your help Anne-Mette!!
Forum: Bioinformatics 02-17-2010, 11:23 PM
Replies: 2
Views: 2,158
Posted By Roald
Hi Junkfish, For a simple, basic and free...

Hi Junkfish,

For a simple, basic and free sequence viewer you might consider the CLC Sequence Viewer available at:
http://clcbio.com/index.php?id=28

Cheers

Roald Forsberg
...
Forum: Bioinformatics 12-03-2009, 03:12 AM
Replies: 2
Views: 1,844
Posted By Roald
Hi Kevin, We are about to release a...

Hi Kevin,

We are about to release a beta-version of our new de novo assembler which is able to assemble large amounts of data on modest hardware. Data can be combined from various platforms and...
Forum: Bioinformatics 11-03-2009, 11:53 PM
Replies: 25
Views: 9,981
Posted By Roald
@drio: to give you an idea about performance on...

@drio: to give you an idea about performance on our setup, please see http://www.clcmachine.com/benchmarks.php Note, that the benchmarks are on our SIMD accelerated softwares, so it may not be...
Forum: Bioinformatics 11-03-2009, 12:56 AM
Replies: 25
Views: 9,981
Posted By Roald
CLC Genomics Machine

Hi drio,

The machine is actually a product that we sell bundled with a full software solution. You can read the full specs of hardware and software at http://www.clcmachine.com/

If you write an...
Forum: Bioinformatics 11-02-2009, 05:14 AM
Replies: 25
Views: 9,981
Posted By Roald
Hi Najim, Due to the large file sizes there...

Hi Najim,

Due to the large file sizes there is a lot of IO going on in NGS bioinformatics analysis. For this reason it is a good idea to purchase a machine with fast discs.

For inspiration, you...
Forum: Bioinformatics 07-08-2009, 01:29 AM
Replies: 33
Views: 16,075
Posted By Roald
454 mapping benchmark

Some benchmarks of how the CLC bio assembler maps 454 reads can be found in the white paper at http://www.clcbio.com/files/whitepapers/white_paper_on_reference_assembly_on_the_CLC_NGS_Cell.pdf
...
Forum: Bioinformatics 06-23-2009, 12:34 AM
Replies: 65
Views: 33,292
Posted By Roald
To Lesley

Thanks for the info Lesley.
Do you happen to have a sample of some tagged Illumina data that I can get?
I basically just need a description of the format so just a few lines from the a file would...
Forum: SOLiD 06-19-2009, 01:57 PM
Replies: 6
Views: 2,273
Posted By Roald
@Ruby, I have no problems loading the website,...

@Ruby, I have no problems loading the website, are you seeing the other pages alright. If you have further problems with the website, please contact support@clcbio.com

@Stegger, thanks for posting...
Forum: SOLiD 06-18-2009, 12:53 PM
Replies: 6
Views: 2,273
Posted By Roald
@Ruby

**Disclaimer: I work at CLC bio**
Hi Ruby,

We have some tutorials on expression analysis that may be of interest to you, you can find these at - http://www.clcbio.com/index.php?id=649

We also...
Forum: Epigenetics 06-18-2009, 12:09 AM
Replies: 13
Views: 7,329
Posted By Roald
@SPGSling

Are you allowing the algorithm to align reads with multiple matches?
If this dramatically increases the number of aligned reads it would indicate problems with overly amplified repeat regions.
Have...
Forum: Epigenetics 06-17-2009, 11:48 PM
Replies: 13
Views: 7,329
Posted By Roald
@SPGSling

What length reads are you aligning and against what reference?

Cheers
Roald

** Disclaimer: I work at CLC bio **
Forum: Bioinformatics 06-16-2009, 03:40 AM
Replies: 65
Views: 33,292
Posted By Roald
To Lesley

Disclaimer: I work at CLC bio
Hi Lesley,

It is correct that there are no options to sort tagged/barcoded Illumina PE data in our current "Multiplexing by tag" functionality. We designed this...
Forum: Bioinformatics 06-15-2009, 02:38 AM
Replies: 65
Views: 33,292
Posted By Roald
CLC Genomics 3.5

Disclaimer: I work at CLC bio
Hi Arne,

I have added some comments to your post here that I hope may be of use:
You are right that the Java side of our software uses a lot of memory. In order to...
Forum: Bioinformatics 06-12-2009, 03:11 AM
Replies: 65
Views: 33,292
Posted By Roald
Workbench issues

** Disclaimer: I work at CLC bio **

Hi Lesley,
I am sorry to hear that you have had some problems getting started with our workbench. I have added a few comments below that I hope are useful to...
Forum: SOLiD 03-19-2009, 02:53 AM
Replies: 22
Views: 42,871
Posted By Roald
Hi RudyS, Thank you for your interest. ...

Hi RudyS,

Thank you for your interest.

We are now at version 3.2 with the Genomics Workbench and I recommend you to get the updated version if you have not done so already.
At the moment we...
Forum: SOLiD 02-12-2009, 12:40 PM
Replies: 22
Views: 42,871
Posted By Roald
You are both absolutely right that a huge amount...

You are both absolutely right that a huge amount of information is lost by aligning SOLiD data in sequence space, rather than in color space.
The benchmarks we have made (see...
Forum: SOLiD 01-29-2009, 12:28 AM
Replies: 22
Views: 42,871
Posted By Roald
Disclaimer: I work at CLC bio We have just...

Disclaimer: I work at CLC bio

We have just included native color space assembly in our NGS cell software
http://clcbio.com/index.php?id=1331

You can grab a white paper with benchmarks at...
Forum: Epigenetics 11-03-2008, 12:32 AM
Replies: 20
Views: 63,496
Posted By Roald
What a great list - thanks a lot for posting!

What a great list - thanks a lot for posting!
Forum: Bioinformatics 09-26-2008, 04:09 AM
Replies: 65
Views: 33,292
Posted By Roald
New CLC Genomics Workbench video: Assembling mixed data sets

Here at CLC bio, we have just produced a small video which shows how you can assemble mixed data sets in our Genomics Workbench 2.0
The data are from two different NGS platforms, Illumina Genome...
Forum: Bioinformatics 09-05-2008, 12:19 AM
Replies: 11
Views: 4,038
Posted By Roald
DeepSAGE using 454 platform

Hi Melano,

If 454 is the platform you will be doing this on, you may wish to explore the DeepSAGE approach for linking tags before pyrosequencing. This way you can increase sampling depth.
The...
Forum: Bioinformatics 08-29-2008, 05:49 AM
Replies: 65
Views: 33,292
Posted By Roald
CLC Genomics Workbench and more

Dear all,

Several people have requested that we wrote an introduction to the CLC Genomics Workbench, so here goes.

Next generation sequencing technologies are causing some dramatic changes in...
Forum: General 08-29-2008, 05:48 AM
Replies: 5
Views: 38,164
Posted By Roald
CLC Genomics Workbench and more

Dear all,

Several people have requested that we wrote an introduction to the CLC Genomics Workbench, so here goes.

Next generation sequencing technologies are causing some dramatic changes in...
Forum: Introductions 08-28-2008, 04:16 AM
Replies: 4
Views: 2,880
Posted By Roald
Thanks ECO and thanks for maintaining this great...

Thanks ECO and thanks for maintaining this great ressource.
Forum: Introductions 08-19-2008, 11:31 PM
Replies: 4
Views: 2,880
Posted By Roald
CLC bio info

Hi Melissa,

Thank you for asking. I am preparing a short piece on our software and some of the thoughts behind it. I will put it in the thread you suggested.

Best regards

Roald
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