Next Generation Sequencing

We have just released a scientific white paper which confirms, that, in benchmarking tests, our new algorithm for assembly of Next Generation Sequencing data is indeed fast. Not only is our algorithm fast, but it also provides a better quality of the results, compared to other algorithms benchmarked in the white paper.

Assistant Professor at Rutgers University, Dr. Todd P. Michael, states,

The speed of CLC bio’s new algorithm for reference assembly of Next Generation Sequencing data raises the bar to a level currently unmatched by any competitor. When CLC bio continues this impressive rate of development, and eventually also handles SOLiD’s Color Space analysis in the same convincing manner, this could easily become a de facto tool for scientists working with Next Generation Sequencing analysis.

The white paper is free to download for everyone at www.clccell.com/ngs

You can read the entire press release by clicking here

I am happy to announce that we have just released version 1.0 of our solution for analyzing and visualizing Next Generation Sequencing data: CLC Genomics Workbench

It includes user-friendly, high quality, high speed reference assembly and de novo assembly of Solexa, SOLiD, 454, and Helicos sequencing data, to name a few key features.

Here you can read a lot more and see a few benchmarks:
http://www.clcbio.com/genomics

Everyone here have worked really hard to make this happen and we now look forward to start coding up new features and functionalities for the next version of the software.

With CLC Genomics Workbench we’re introducing a new assembly pipeline, which is not only sophisticated and highly scalable - but also very fast. In benchmark tests we have assembled half a million 454 reads against the full E.coli reference genome, in around 2 minutes on a Dual-core laptop with 1 gigabyte RAM, which is very fast compared to similar solutions in the market. This speed-up increases when using a computer with more cores and RAM.

A normal computer processor does one calculation at a time at a very high pace, which is ideal for a lot of work. With bioinformatics you often experience the need to do repeat calculations with large data sets, so ideally you want to do calculations in parallel. The software acceleration in CLC Genomics Workbench is done through a high-performance computing technology called SIMD (Single Instruction, Multiple Data), which enables a standard computer processor to execute similar calculations in parallel. So instead of doing one calculation at a time, you can do multiple and thereby greatly speed up the computing process.

When doing reference assembly of Next Generation Sequencing data, you essentially need to compare a vast amount sequence reads to a single reference genome, which makes it highly ideal to use parallel computing techniques. And that’s exactly what we have done with CLC Genomics Workbench to make the Next Generation Sequencing assembly as fast as possible.

That’s our little/fast secret!

Boston, USA — April 25, 2008 — On Monday, April 28, CLC bio will officially unveil their new Next Generation Sequencing solution, CLC Genomics Workbench, the first comprehensive analysis package which can analyze and visualize data from all the major Next Generation Sequencing (NGS) platforms, such as SOLiD from Applied Biosystems, 454 GS flx from Roche Applied Science, Solexa from Illumina, and HeliScope from Helicos. The World Premiere is at the Bio-IT World Conference & Expo,April 28 - April 30, at the World Trade Center in Boston, USA.

Vice President of CLC bio, Jan Lomholdt, states

Having experienced massive pre-release interest from people within the Next Generation Sequencing segment, we’re confident that our cross-platform NGS solution which includes an intuitive graphical interface, numerous downstream analyses, and support for all the major NGS platforms, will become a hit. Especially when taking into consideration that we have assembled half a million 454 reads against the full E.coli reference genome, in around 2 minutes on a Dual-core laptop with 1 gigabyte RAM. In other words: This is FAST!

Bio-IT World Editor-in-Chief Kevin Davies, PhD, adds

There is an explosion of interest in the next generation sequencing field right now, and I’m confident that CLC Genomics Workbench will become a valuable tool for the rapidly growing number of users in academia and industry who are using these new instruments for an amazing range of applications. We’re also delighted that CLC bio has chosen this year’s Bio-IT World Expo in Boston to announce and introduce this product to the scientific and informatics communities.

CLC Genomics Workbench includes accelerated assembly of Next Generation Sequencing data through use of High Performance Computing technology, making the assembly process very fast. The genomes to be assembled can be of any size, only limited by the number of gigabytes of RAM available on the computer running the assembly.

CLC Genomics Workbench takes full advantage of “paired end” data, and supports a number of features and work-tasks, such as reference assembly of genomes, De Novo assembly of genomes, SNP detection using advanced statistical models, Digital Gene Expression, metagenomics, clustering and assembly of EST and cDNA sequences, large amounts of genomics and transcriptomics downstream analyses, and workflow support. Some of the mentioned features will be implemented in future releases.

CLC Genomics Workbench has already been chosen as Next Generation Sequencing platform for all Danish universities. CLC bio will release CLC Genomics Workbench to the public in late May. To read more about CLC Genomics Workbench go to: www.clcbio.com/genomics

Here you can watch a 6-minute preview of the most ambitious platform for Next Generation Sequencing analyses: CLC Genomics Workbench. This software package is the only to support all current NGS formats: 454, Solexa, SOLiD - and later on Helicos, among more.

This video preview shows a few of the features - more are already implemented in the workbench - and you can learn a bit about the intuitive graphical user-interface to access this extremely powerful Next Generation Sequencing analysis package.

To watch the movie at YouTube.com, click here.

If you’re interested in learning more about CLC Genomics Workbench - or would like to sign up for a trial version - you can click here!