Posts Tagged ‘CLC Bio’

Curator: Aviva Lev-Ari, PhD, RN

Dr. M. Michael Barmada, Associate Professor at Center for Computational Genetics, University of Pittsburgh, tells about how the hot topic of the times now – genetics – has challenged the computational resources across the University:

Associate Professor at Center for Computational Genetics at University of Pittsburgh, Dr. M. Michael Barmada

CLC bio Annual Survey Results


CLC Bio has published the results of a survey of researchers in the next-generation sequencing market to find out which sequencers and software are used the most.

The company says it received responses from 708 individuals in 73 countries.

Not surprisingly, they found that Sequencers

  • Illumina’s HiSeq and MiSeq are the most used instruments with about 34.6 percent and 21.3 percent of respondents, respectively, stating that they use the systems. Meanwhile,
  • Roche’s 454 sequencers got 21.2 percent of the votes and
  • Life Technologies’ Ion Torrent Personal Genome Machine got 11.5 percent of the responses.

In terms of Bioinformatics tools, the

  • UCSC Genome Browser has the most use, according to the survey, with 28.9 percent of respondents reporting that they use the program. Next in line is
  • Ensembl tools and then – 26.9
  • Bowtie with  23.4 percent of the votes, respectively.

Also worth noting is that NGS is being used primarily for

  • whole-genome sequencing — 40.8 percent of the votes — followed by
  • RNA-seq and — 40.1 percent
  • de novo sequencing with  39.8 percent of the votes, respectively.

Of the 708 respondents, about 24.6 percent work in the US, according to CLC. Also,

  • 73 percent of respondents work in academic research while
  • 9 percent work in industry, another
  • 9 percent in government, and
  • 6 percent work in not-for-profit organizations, according to the survey.
We believe MedQL has the potential to be an effective time saver for researchers working with variant prioritization, making it a promising new plugin for CLC Genomics Workbench. We’re excited to add BioQL’s technology for evidence-based downstream analysis of Next Generation Sequencing data to our products.
Director of Global Partner Relations at CLC bio, Mikael Flensborg
Using CLC Genomics Workbench, a common workflow to detect causative mutations in medical genomics involves read mapping and variant detection. The result is a list of candidate gene variants that differ from the reference genome. The MedQL plugin uses an evidence-based approach to prioritize these genes for functional studies and, thereby, allowing researchers to focus their efforts on the most promising candidates.


Aarhus, Denmark — November 7, 2012 — Today, CLC bio and the independent software vendor, BioQL, announced the release of the MedQL Variant Prioritizer plugin for CLC Genomics Workbench. The plugin connects with MedQL’s online database to prioritize a list of variants in gene regions based on their degree of association with a given phenotype.

The MedQL database contains more than 20 million articles from Medline, indexed using a dictionary of nearly 300,000 terms from authoritative ontologies such as the HUGO Gene Nomenclature Committee (HGNC), the Human Disease Ontology, and the Online Mendelian Inheritance in Man (OMIM).


We’re the world’s leading bioinformatics software developers and the only ones providing an analysis platform where both desktop and server software are seamlessly integrated and optimized for best performance.

Our wide range of analyses are available both through a user-friendly graphical user-interface as well as through command-line, allowing scientists to choose their preferred interface.

By developing our own proprietary algorithms, based on published methods, we have successfully accelerated the data calculations to achieve remarkable improvements in speed over comparable solutions.

Our enterprise platform serves as the backbone of sequence analysis pipelines for a large number of the world’s most prominent research institutions. With around 2000 different organizations as our customers around the globe, including the ten biggest pharmaceutical companies in the world, we have established ourselves as the market-leader in sequence analysis software.

One of our key strategies is to be ‘cross-platform’, which means we support all the major next generation sequencing platforms as well as traditional Sanger-based sequencing, effectively giving our customers a one-stop-shop for their analysis needs across all sequencing platforms.


 Desktop software for Sequence Analysis based on an overall level of subjects.


Next Generation Sequencing analysis
Transcriptomics (Gene expression features also available in CLC Main Workbench)
RNA secondary structure
BLAST searches
Protein analyses
Primer design
Assembly of Sanger sequencing data
Molecular cloning
Pattern discovery and motif search
Nucleotide analyses
GenBank Entrez searches
Sequence alignment
Phylogenetic trees
Detailed history log
Batch processing
Customization of your workbenches

CLC Genomics Machine

Our turnkey solution, for small research labs. It includes CLC Genomics Server and CLC Genomics Workbench. Everything is preinstalled on a powerful desktop computer or server blade – ready to plug-in and run from the day it is delivered.

CLC Genomics Factory

Our turnkey solution for medium and large research labs that needs a complete IT infrastructure for their NGS data analysis.


Our software is made for biologists by biologists, so it’s easy to analyze, visualize, and compare DNA, RNA, and Protein data, as well as run advanced workflows with large and complicated datasets.


Aarhus, Denmark — January 8, 2013 — Today CLC bio, the global leader in commercial sequence analysis software, announced that the J. Craig Venter Institute (JCVI) has extended their site license agreement with CLC bio through 2017.

JCVI has been utilizing CLC bio’s enterprise platform since 2009 and currently uses it on more than 30 research grants, including their work as part of the Human Microbiome Project (HMP). The HMP is a National Institutes of Health-funded project to catalogue and characterize the microbes living in and on the human body. Recently, the HMP Consortium published a series of papers with results from this work in Nature and PLOSone. CLC’s bio software was used in the analysis of this work.

The complexity and diversity of our research projects necessitates unique tools to analyze these increasingly large data sets. In our pursuit of excellence we always test and employ the best available tools for our research projects. As such we’re happy to announce the extension of our site license with CLC bio through 2017.
Karen Nelson, Ph.D., President, JCVI
For us, it’s always very exciting to see the results of all the intriguing research that our customers are doing, and no less so, when JCVI published their papers on the HMP project this summer. JCVI was one of our first site license deals with a premier institution in the genomics research field, and we’re proud to announce it has been extended for another five years.
Thomas Knudsen, CEO, CLC bio

The original 4-year site license agreement between JCVI and CLC bio was signed in the summer of 2009, and has now been extended by another 5 years, through 2017. JCVI deploys CLC bio’s platform in an integrated environment across multiple geographical locations and together with international collaborators.

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