Next Generation Sequencing

A lot of people are looking into buying a next generation sequencer these days and weighing the pros and cons. People are obviously attracted to the idea of expanding their research capacities with high throughput sequencing but at the same time they are worried about the skills and resources needed to run the instruments. As a company we are trying to bring out solutions that alleviate the bioinformatics obstacles in the process.

Genome Technology have recently posted an article which discusses some of the challenges facing the purchasers of NGS instruments.

Boston, USA — April 29, 2008 — Today at the Bio-IT World Conference & Expo in Boston, USA, CLC bio announced collaboration with Microsoft Corp. on integrating CLC bio’s extensive bioinformatics solutions with Microsoft’s software platform, for the benefit of companies, corporations, and institutions in the biotech, pharmaceutical, and life science sectors. CLC bio has already added support for Microsoft SQL Server in its database solution, CLC Bioinformatics Database, as well as support for Microsoft’s high-performance computing solutions, Windows Compute Cluster Server 2003 and Windows HPC Server 2008.

Dr. Rudy Potenzone, worldwide pharmaceutical industry technology strategist at Microsoft Corp. and director of the Bio IT Alliance, states

We are delighted to work together with CLC bio, a member of the Bio IT Alliance and one of the world’s leading bioinformatics solution providers. This collaboration will ultimately help life sciences firms transition to the Microsoft platform throughout their research and development departments. CLC bio’s tools, fully integrated with the Microsoft Office System, increase ease of use and expand the number of potential users, while reducing administrative overhead and creating a lean workflow. Furthermore, CLC bio’s internationally renowned experts are available for consulting and customized development.

Jan Lomholdt, Vice President at CLC bio, continues

With our support for Microsoft’s server solutions, the first step in the process has already been taken. The second step is to further advance our collaboration in areas such as Next Generation Sequencing and high-performance computing, which ultimately can help realize the potential of personalized medicine. As a former member of Microsoft’s World Wide Advisory Council, I have first hand experience of the strength and potential Microsoft brings to the table with a collaboration like this, which of course is interesting for a company like ours.

Windows HPC Server 2008, the successor to Windows Compute Cluster Server 2003, includes a common set of High Performance Computing productivity tools that reaches across desktop and clusters, including a new Parallel Computing Initiative for multicore development. CLC bio’s high-performance computing solution for servers and clusters, CLC Bioinformatics Cell, supports Microsoft’s Message Passing Interface (MPI) in order to run bioinformatics algorithms such as HMMER, ClustalW, and Smith-Waterman on Windows HPC Server 2008 installations.

All CLC bio’s solutions are cross-platform, running on Windows 2000, Windows XP, Windows Vista, as well as Mac OS X and Linux.

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

Researchers from Baylor College of Medicine sequenced the genome of James D. Watson.
It took them 2 months and 234 sequence runs on a 454 GS FLX System to complete this task. They found 29 Mb of sequence to be absent from the reference genome containing several new genes.

You can find the details in this Nature paper.

GATC Biotech AG have announced their purchase of another 454 GS FLX system. This adds to the company’s NGS portfolio which already includes systems from 454, Solexa and SOLiD.

According to the press release, GATC’s site in Constance now has a sequencing capacity of 450 gigabases per year.