The ultimate NGS platform for Molecular Labs

An high-throughput sequencing blog from the scientists at CLC bio

We will be conducting a workshop on NGS data analysis and visualization at the Plant and Animal Genome Conference XX in San Diego, January 17, 2012.

We will present an overview of CLC Genomics Workbench, and cover the features of de novo assembly, RNA-Seq, and our resequencing tool using Genomics Gateway in more detail. Genomics Gateway is our new framework for visualizing, combining and analyzing whole genome data.

Our invited speakers - Prof. Juan F. Medrano, Animal Genomics Laboratory, UC Davis and Prof. Claude dePamphilis, Biology Department, Penn State University - are recognized experts within the field of genomics, and will provide their inputs on how they use our tools in their research.
Please join us for interactive presentations from 1:30 to 3:40 pm on January 17 in the Golden West room at the Town and Country Convention Center in San Diego.

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07 2011
Survey draw for an iPad
Tag: Misc. — Goerlitz @ 20:53
In November month’s newsletter we launched a survey where all respondents would enter a draw for an iPad. Yesterday we found the winner and it’s Michael Lauck from David O’Connors lab at the University of Wisconsin-Madison - congratulations!

Here’s a couple of insights from the survey:

Academic 70.4%, Biotech 7.8%, Pharma 0.9%, Governmental 8.3%, Medical 6.2% and Other 6.4%
58% of all the respondents work with NGS analysis an a regular basis
18% have one in-house NGS instrument, whereas 29% have between 2-5 instruments. 5% have more than 5 instruments and the rest didn’t have any!

Thanks to everyone who participated!
Michael Lauck

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29 2011
Recent Nature publication on the Medicago truncatula genome references CLC bio
Tag: Publications — crasmussen @ 12:10
An international group of researchers presents here the draft sequence of the M. truncatula euchromatin. The studies are based on combined data sets from BAC assembly and Illumina shotgun sequence, in total capturing ~94% of all M. truncatula genes.
Medicago truncatula is a long-established model for legume biology studies and analysis of the genome sequence can provide valuable information.
Methods of the studies included DNA sequencing, and assembly of sequencing reads were partly done using CLC bio.

If you are interested in learning more about this research, you can read the full article here

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07 2011
Popular free 6-months licenses for owners of benchtop sequencers
Tag: Misc. — Goerlitz @ 00:55
In July we launched an initiative to support all the researchers investing in benchtop sequencers, like Ion Torrent from Life Technologies, GS Junior from Roche 454, or MiSeq from Illumina. Basically we offer one 6-months license of our premier desktop software package, CLC Genomics Workbench, to researchers and organizations who have bought one of these instruments.

The initiative has gotten a lot more traction than we originally anticipated, which we’re really happy about. Also, we think this is a good indication that the next generation sequencing technology is being democratized, in the sense these machines are being purchased by a lot of organizations who haven’t operated next generation sequencers before.

If you’re interested in learning more and maybe even enter our quarterly competition to win a permanent license, please check out

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16 2011
Looking for a new job?
Tag: Misc. — Goerlitz @ 09:53
All over the world, we experience tremendous growth in the use of our platform for DNA sequence analysis - especially for high-throughput sequencing data. As a result of this, all our divisions are fast growing and we have an ongoing search for talented people to join us here in our ambitious and fast-growing company! Just this past month, we have increased the number of employees by almost 10% - and we still have many open positions both in Europe, America, and Asia.

Most of our divisions are currently looking to recruit - including Software Development, Sales, and our world famous Support - and we’re looking to hire people in different parts of the world.

If you’re curios to learn more about what it would be like to join our innovative team and make a difference, we encourage you to have a look at the “careers” section on our website - and if your ambitions and skills match any of our job postings, we hope to hear from you soon:

Start now

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Digital Transformation

Sequencing of the most impressive snake - the king cobra
Tag: Misc., Research — crasmussen @ 19:44
The genome of the worlds largest venomous snake, the king cobra, has been sequenced and analysed by researchers from the Dutch company ZF-screens.

Looking for interesting pharmaceutical compounds, they have been using our de novo assembler for analysing the sequencing data gained from the genome of this impressive snake.

Dr. Ron Dirks, Research Manager at ZF-screens, tells us about the project, some of their very interesting findings and future aspects of the research.

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16 2012
Medical Resequencing pipelines, Trio Analysis, and Streamlined Amplicon sequence from NGS Data
Tag: Misc. — alykkebak @ 12:03
Are you attending to ASHG 2012?

Mark your calendar for science and medical genomics with CLC bio, Friday November 9, from 12.45 - 2.15 pm!
Join us when guest speakers (such as Dr. Michael Barmada from Pittsburgh University), will share insights about their research and how to overcome challenges when working with medical genomics, like medical re-sequencing pipelines, trio analysis, and streamlined amplicon sequence from NGS Data.

Our final program with all the guest speakers will be announced in the fall.

The meeting takes place at the Moscone Center, Mezzanine Level, Room 236/238.
Everyone is welcome to attend.

/If you have any questions about this event, please contact us:

Please check out for more information about CLC bio and medical genomics.

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05 2012
Casual pizza’n'beer workshop introducing CLC bio’s SDK
Tag: Development, Misc., Publications, Research, Technology, Updates — crasmussen @ 13:52
Join us for a casual workshop introducing how to use our SDK to create plugins - and stay for pizza, beer, and a fun quiz with cool prizes!

The program is centered around four external speakers from Convey (US), Bioformatix (US), NICTA (AUS), and Ablynx (BE), who all have used our API for different kinds of integrations, including examples of commercial plugin development. You can also learn how to distribute your own algorithms and workflows to our customer community through plugins for our platform.

Quiz with cool prizes
We’ll round off the evening with a quiz where teams of three can participate and win cool prizes, such as the ASUS TF700T, an iPad 3, a Lytro camera, a Sphero ball, as well as other cool stuff. It’ll be fun and there’s a good chance to win something, as we only have seating for 50 people - first come, first served, when we open the doors at 6 PM! Bring your ISMB badge to get in, as long as we have seats.

Hope to see you this Sunday in Long Beach!
Don’t miss this workshop on Sunday the 15th of July, from 6 to 10 PM. You’ll find the workshop in rooms E-F on the 3rd level at the Hyatt Regency Long Beach. You don’t have to register, but there’s only 50 seats…


Intro - Mikael Flensborg, CLC bio
How a plugin can make the difference - Marc Logghe, Ablynx
High-performance computing for genomic data analysis workflows - George Vacek, Convey Computers
Software distribution partnerships - Mikael Flensborg, CLC bio
Analysis of differential expression in microarray experiments with Bootstrapped ROC plugin - Dariusz Wroblewski, BioFormatix
Tools for Genome-Wide Search for Epistasis and In-silico Regulatory Variant Discovery - Adam Kowalczyk, NICTA
Epilog - Mikael Flensborg, CLC bio
Pizza, Beers & Quiz - Lasse Görlitz, CLC bio
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04 2012
White paper on our new Probabilistic Variant Caller shows excellent performance
Tag: Development, Publications, Technology, Updates — crasmussen @ 13:17
With our latest beta release - and final release of CLC Genomics Workbench and CLC Genomics Server in August 2012 - we introduce a new Probabilistic Variant Caller calling variants like SNVs, insertions, deletions and MNVs (Multiple Nucleotide Variants) from a read mapping using a probabilistic model. In comparison to other available variant callers, it can detect variants in data sets from haploid (e.g. bacteria), diploid (e.g. human) and polyploid organisms (e.g. cancer and higher plants) with a high sensitivity and specificity.

The white paper includes a detailed explanation of the algorithm behind the Probabilistic Variant Caller as well as the results of a performance benchmark for the variant caller performed on an E. Coli paired-end Illumina dataset and two Homo sapiens Illumina datasets to measure the specificity and sensitivity of the algorithm, respectively.

The Probabilistic Variant Caller shows a specificity of more than 99.99% when tested on an E. coli dataset. Tweeking the ploidy parameter and filtering for variants having a low average base quality, the specificity can even be increased to 100%.
The variant caller was also compared against two human datasets available from Illumina and GATK to show the sensitivity in comparison to both the Casava variant caller provided from Illumina and the UnifiedGenotyper tool provided from GATK. The results demonstrate excellent performance of our variant caller in comparison to other commonly used variant callers for haploid and diploid genomes, and in addition we provide the ability to call variants in polyploid organism as well.

Click to read the white paper on Probabilistic Variant Caller 1.0

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12 2012
Completely new re-sequencing pipeline released in beta
Tag: Misc. — crasmussen @ 10:24
Our development team has been working hard for months to give you this large update of CLC Genomics Workbench. The final release will be in August 2012, but if you want, you can already try the beta version now.

To give you a full overview, Søren Mønsted, who is our Manager, Product Development, has recorded a small video highlighting the most important news in this release.

Here’s a quick summary:
* New read mapper with amazing performance (color space mapping is still using the old mapper)
* New probabilistic variant caller
* A whole suite of tools for downstream annotation and comparative analysis of re-sequencing data (based on the Genomics Gateway plug-in that has been out in beta for some time)
* Introducing tracks as the new concept for genomic data analysis
* Workflow support: create your own workflows and install these in the Workbench, send to a colleague or install on CLC Genomics Server.

Please download and try CLC Genomics Workbench Beta 5.5 here.

NB. We will of course try to fix any problems as soon as possible but please remember that this is a beta release and you should not rely on this for your daily work.

Download the Beta version of CLC Genomics Workbench
See a full list of improvements
Click here if you are interested in more information about CLC Genomics Server
If you already have a CLC Server installation and want to try the new beta version of the Server, please contact


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