Next Generation Sequencing

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!

Aarhus, Denmark and Pretoria, South Africa — February 12, 2008 — The world’s leading bioinformatics solution provider, CLC bio, has joined forces with the first center for High Throughput DNA Sequencing in Africa, Inqaba Biotechnical Industries (Pty) Ltd., in an effort to help fight tuberculosis on the African continent. Together CLC bio and inqaba biotec will assemble and analyze data from multiple tuberculosis strains, sequenced on inqaba biotec’s Genome Sequencer FLX system.

CLC bio, is in the final stage of development of their upcoming CLC Genomics Workbench, which is a new workbench aimed at next generation sequencing and whole genome assembly. The new workbench will support all next generation sequencing platforms, such as Roche GS FLX (454), Illumina Gene Analyzer System (Solexa), and SOLiD Analyzer from Applied Biosystems from the start - with Helicos and others to be included in the near future.

Dr. Oliver Preisig, Executive Director at Inqaba Biotechnical Industries, states,

The consortium’s goal is to find the genetic differences between different strains of Mycobacterium tuberculosis. We target our genome sequencing on XDR (Extreme Drug Resistant) and MDR (Multi Drug Resistant) strains of the bacterium. Having assembled the genomes of these strains we can find the strains’ specific markers and develop a PCR test that could bring much faster diagnosis for proper treatment. This means we have an urgent need for whole genome sequencing, and look forward to CLC bio’s upcoming workbench, which will provide an intuitive and fast solution.

Senior Scientific Officer at CLC bio, Dr. Roald Forsberg, continues,

We are really exited to join forces with inqaba biotec in their Tubercolosis research program. The large amount of genomic data inqaba biotec produces offers us an exciting opportunity to test and fine tune our algorithms on real and challenging data - and at the same time it allows us to contribute to the ongoing fight against Tuberculosis. This is a great motivation to our developer team.

The South African Mycobacterium tuberculosis genome sequencing project is funded by BioPAD, a biotechnology investment trust funded by the Department of Science and Technology of South Africa and includes as consortium members the Chris Hani Baragwanath business unit of the National Health Laboratory Services, the Respiratory and Meningeal Pathogens Research Unit at the University of Witwatersrand and inqaba biotec.

The upcoming CLC Genomics Workbench will among other things feature an SIMD accelerated genome assembler, and will take full advantage of “paired ends” data. CLC bio will release CLC Genomics Workbench in the spring.

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms. CLC bio is an Apple value added reseller.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

• Development of bioinformatics software and hardware based on the latest scientific findings
• User-friendly, integrated and intuitive cross-platform software solutions
• Continuous focus on customer needs and superior customer service
• Frequent product updates including the latest IT technologies and bioinformatics algorithms
• A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

About inqaba biotec

Inqaba Biotechnical Industries (Pty) Ltd, trading as inqaba biotec, is a private South African genomics company founded in 2002. inqaba biotec was initiated and funded by a few scientists from South Africa, the USA, Germany and Switzerland. inqaba biotec is based in Pretoria, South Africa. A Swiss government loan with the aim of facilitating investments in developing and emerging countries was crucial in the start-up years. At the end of 2005 BioPAD (www.biopad.org.za), a biotechnology investment trust funded by the Department of Science and Technology of South Africa, joined inqaba biotec as a shareholder and strategic partner. inqaba biotec’s customer base covers the whole of South Africa as well as other Sub-Saharan countries. In March 2007, inqaba biotec started offering a genome sequencing service using first a GS 20 and later a GS FLX from Roche as part of an infrastructure investment by BioPAD.
For further information, please visit inqaba biotec’s website www.inqababiotec.co.za

Aarhus, Denmark — January 17, 2007 — CLC bio and several prominent Danish research institutions have established SEQNET - a national network for developing a unique software platform for the analysis of data from the next generation sequencing technologies. The platform will integrate groundbreaking bioinformatics algorithms with a user-friendly and graphical user interface. The network is funded by the Danish Agency for Science Technology and Innovation, with a total of three million USD and will initially operate for three years, starting January 2008.

Senior Scientific Officer at CLC bio, Dr. Roald Forsberg, states,

Next generation sequencing technologies, like 454, Solexa, or SOLiD are pushing a revolution in genetic analysis. Their massive throughput has given rise to a plethora of novel applications for DNA sequencing and has dramatically increased the ambitions of existing projects. However, handling the large amounts of fragmented data presents a great bioinformatics challenge to be dealt with before researchers can get the full value of these new technologies. Since DNA sequencing is becoming omnipresent in research we believe that the answer to this challenge is a unified next generation sequencing platform. In this network, we will make such a platform come together by combining our unique capacities for producing graphical user interfaces, algorithms and high performance computing solutions with the expertise of Denmark’s foremost researchers in the field.

Head of the Danish SEQNET project and Associate Professor at the Department of Life Sciences at Aalborg University, Dr. Kåre Lehmann Nielsen, continues,

We’re fortunate to be able to establish this national network with one of the leading bioinformatics companies in the world, CLC bio. They bring a very high level of understanding and experience in working with cutting edge technology and advanced algorithm design. With their multifaceted workbench structure, CLC bio will provide a stabile and user-friendly platform for this project. During the project, the tools developed will be tested and refined through a wide variety of different research projects, ranging from tag-based expression analysis and metagenome analysis of sludge, to cancer cell characterization, ensuring the solution will receive first-class input from all the finest experts in Denmark.

A significant amount of new or optimized bioinformatics algorithms will be developed in this project. They will all be bundled into a comprehensive bioinformatics package based on CLC bio’s present platform, the workbench, facilitating analysis of new sequencing technology data by research groups in companies and large corporations, as well as public and private research institutions.

The founding partners of the Danish SEQNET, of which four sites already have invested more than four million USD in next generation sequencing equipment in 2007, are Department of Life Sciences at Aalborg University, Faculty of Agricultural Sciences at Aarhus University, Department of Biology at University of Copenhagen, University of Southern Denmark, Aalborg University Hospital, and CLC bio.