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Thread | Thread Starter | Forum | Replies | Last Post |
CLC Genomics Workbench - Windows vs. Linux | figure002 | Bioinformatics | 24 | 12-06-2013 06:10 AM |
Getting a full annotation onto a consensus sequence in CLC Genomics Workbench | Dapip33 | Genomic Resequencing | 1 | 09-19-2013 07:02 AM |
CLC Genomics Workbench for de novo RNA-seq | JQH | Bioinformatics | 1 | 07-12-2011 11:17 PM |
CLC Genomics Workbench goes hand in hand with Ion Torrent data | CLC bio | Vendor Forum | 0 | 05-12-2011 05:34 AM |
Mapping RNA seq using CLC Genomics WOrkbench | rururara | Bioinformatics | 1 | 02-22-2011 11:35 AM |
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#1 |
--Site Admin--
Location: SF Bay Area, CA, USA Join Date: Oct 2007
Posts: 1,358
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Hasn't been released yet, should be interesting to see. I will definitely be signing up for a trial.
http://www.clcbio.com/index.php?id=1240 |
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#2 |
Senior Member
Location: Monash University, Melbourne, Australia. Join Date: Jan 2008
Posts: 246
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Yes, I'm waiting for that too... I hope it's as good as they're saying it will be. The initial release is supposedly able to do de novo assemblies on all sanger, illumina and 454 data, which would be nice.
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#3 |
Senior Member
Location: The University of Melbourne, AUSTRALIA Join Date: Apr 2008
Posts: 275
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The recent version of MIRA claims to be able to perform a true hybrid assembly of sequences from Sanger, 454-FLX, and Illumina. We are still assessing it. See http://chevreux.org/projects_mira.html
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#4 | |
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Location: Germany Join Date: May 2008
Posts: 79
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#5 |
Junior Member
Location: Edinburgh, UK Join Date: Jun 2008
Posts: 1
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I just heard from the CLC Bio sales rep that the Genomics Workbench has been released.
http://www.clcbio.com/index.php?id=1296 This page has links to their user manuals - which look good. If they do what they say on the box, then I can imagine lots of people would be happy to pay up a bit even though it is not a published/open-source system. I've asked for an evaluation copy and will post a review over here for everyone if I get it soon. - Sujai |
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#6 |
Senior Member
Location: USA Join Date: Jan 2008
Posts: 482
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Yes it is interesting...I am eagerly waiting to hear back
NextGENe demo talk was impressive - they have a way to somewhat assemble the reads and use the longer contigs to align to reference - irons out errors CLC video was interesting as well .. but click click interface! how well does it work for core labs? |
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#7 |
Junior Member
Location: Bethesda, MD Join Date: Jul 2008
Posts: 6
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I got a trial copy of CLC Bio Workbench. They only let you use their trial data sets. You can't upload your own. Its pretty efficient. It mapped 5 million paired-end solexa reads on my Mac book pro in an hour. It doesn't have all the capability I'd like but I wasn't able to try it on my data.
__________________
Wes Beckstead Predoctoral Fellow in Bioinformatics Boston University Partnership with NIH becksteadw@mail.nih.gov |
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#8 |
Senior Member
Location: Monash University, Melbourne, Australia. Join Date: Jan 2008
Posts: 246
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If you call them or email them, they'll allow you to trial it with your own data. You have to discuss the project with them, first, though.
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#9 |
--Site Admin--
Location: SF Bay Area, CA, USA Join Date: Oct 2007
Posts: 1,358
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Just had their training/intro this morning. Looks pretty powerful, I'm downloading the trial now.
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#10 | |
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Location: Seattle, WA Join Date: Apr 2008
Posts: 84
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#11 |
Director at CLC bio
Location: Denmark Join Date: Aug 2008
Posts: 26
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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 the high-throughput sequencing landscape and in turn generating a lot of challenges to the field of bioinformatics. The Genomics Workbench was created to address these challenges. The objective of the CLC Genomics Workbench is to create an integrated bioinformatics environment which combines the power to handle the magnitude of NGS data with a carefully designed graphical user interface. For the first version we have focused on handling the secondary level of NGS bioinformatics, namely de novo assembly and reference assembly. However, we have also included some tertiary analyses like SNP detection and graphical identification of large scale genomic events. For a full feature list, have a look here. Version 2.0 of the software is out in a few days, and for this release we have focused on bringing our Workbench to a state where it can comfortably handle human genome size data sets. This includes the following improvements:
Alongside Genomics WB 2.0, we are also releasing a command line program package for de novo and reference assembly which will give users access to these tools in a scripting environment. This package is a separate product which includes the fast assembly algorithms and a number of utilities for handling assembly results. Having established a firm basis for secondary analysis we have an ambitious roadmap for including more tertiary analysis tools later this year. These include:
Further down the line we are looking at including features like:
However, although we intend to provide a very comprehensive tool set we know that we can not cover all applications there is. For this reason, we are focusing on providing an open industry-strength platform that users can modify and extend. For this reason we provide a Software Developer Kit which gives access to an extensive and well supported API and a developer community. I hope this was of help and please feel free to post any questions or comments to this that you may have. Cheers Roald |
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#12 |
Director at CLC bio
Location: Denmark Join Date: Aug 2008
Posts: 26
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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 Analyzer and 454, and contains both paired-ends and single reads. Comments are much appreciated. You can view the video here. Best regards Roald Forsberg, CLC bio. |
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#13 |
--Site Admin--
Location: SF Bay Area, CA, USA Join Date: Oct 2007
Posts: 1,358
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What! SEQanswers is not in your blogroll?!
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#14 |
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Location: new york Join Date: May 2008
Posts: 20
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ECO et al.
The CLC Genomics Workbench has been available for over a year and I notice that many people signed up to test it ... have people continued to use it (paying customers)? any opinions on their de novo assembler? any suggestions on selecting penalties etc? RudyS |
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#15 |
Senior Member
Location: The University of Melbourne, AUSTRALIA Join Date: Apr 2008
Posts: 275
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RudyS,
The department I work within spent a fair amount of time evaluating it, and recently purchased a few full licences. CLC was generous with temporary licences throughout the process. Our main application area is prokaryotic sequencing and transcript analysis using Illumina GA2, so de novo assembly and SNP reporting was important. We also tried it on a mixture of Win32, Win64, Mac OS X and Linux64 machines - ranging from single core 2 GB to 8 way 64 GB RAM machines. Traditionally we have used Velvet for assembly, Shrimp/MAQ for SNP analysis, and Artemis and in-house applications and scripts for the rest. We found the CLC "de novo" assembler to be very slow compared to Velvet. The results were similar to what Velvet gave (based on some resequencing results). The main issue is that the CLC de novo assembler did (or does still?) not support PAIRED END assembly (unlike Velvet). It appears it does by the way the GUI presents it, but tech support confirmed it doesn't use it to link contigs. It does show you the paired ends mapped to the result though. We didn't use the reference assembler much. The SNP reporting works well once you tell it to do 'gapped alignment' but it did miss some things we found with Shrimp, but that could be parameter setting issues. The RAM usage of CLC was quite huge when loading 1 or 2 lanes of Illumina data. It seemed to need more RAM on the Linux versions than Windows. The Linux versions were problematic with earlier versions we tried, but they did fix some issues. As stated earlier, CLC needed much more CPU time - but it was capable of multithreading for some assemblies, but Velvet was still way faster. The main benefit of buying CLC is to "empower" the biologists to explore these data sets themselves. The open source available software just isn't ready for use by non-bioinformatics/I.T people. --Torst |
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#16 |
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Location: Copenhagen Join Date: Nov 2008
Posts: 21
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Hi Torst,
did you see any significant improvements in terms of speed in the 3.2 release from March? They stated that it was significantly faster (like 25%). Last edited by Stegger; 04-01-2009 at 12:18 AM. |
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#17 |
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Location: new york Join Date: May 2008
Posts: 20
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Stegger
One thing different in the new release is that there is no longer a minimum contig length of 200 bases ... strangely enough I am now getting "contigs" in de novo assembly of 36 bases ... from 36 base solexa reads ! ... this seems to be a glitch ... my problem with CLC is related to connecting contigs that "by eye" have plenty of coverage at overlapping regions but CLC wont connect them ... the penalty adjustments dont seem to do anything significant ... mismatch penalty of 2 gives basically the same result as mismatch penalty of 1 for de novo assembly ... with velvet there is a large difference in the contig size when you reduce the coverage_cutoff ... other problems, like accuracy, are introduced with reduced coverage_cutoff but at least it acts as one would expect ... with CLC, staring at some of the contig ends after blasting them on what for sure is where they come together, and then looking at the read coverage in the unjoined region, it is hard to understand what kept the assemler from joining them into a larger contig ... on the other hand, CLC does give you the graphic that neatly lines up all the reads so you have the opportunity of looking at them to try to understand how it made its decisions ... as Torst points out, the many helpful graphic utilities with CLC (presumably the reason it is slow?) make the experience more pleasant ... Rudy |
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#18 | |
Senior Member
Location: The University of Melbourne, AUSTRALIA Join Date: Apr 2008
Posts: 275
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The main issue is that there is no true objective criterion for comparing de novo assemblies when no close references are available. |
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#19 |
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Location: Copenhagen Join Date: Nov 2008
Posts: 21
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Thats true. I have the Genomics program and are really happy with it, but I am also mostly a molecular biologist with an interest into bioinformatics but no expert. So I like the interface and options in provides me in a somewhat familiar interface.
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#20 |
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Location: Copenhagen Join Date: Nov 2008
Posts: 21
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