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.
Abstract
With Next Generation Sequencing (NGS) technologies, High Throughput Sequencing has become accessible to a much larger group of researchers. NGS technologies therefore have the potential to transform biomedical research and eventually also health care areas such as molecular diagnostics and personalized medicine.
However, High Throughput Analysis has not become commonly accessible yet, and therefore data analyses represents a serious bottleneck, which prevents scientists from reaching the full potential of the NGS technologies.
In these sessions, I will give you our perspective on the bioinformatics challenges arising from NGS data and how we are addressing these to make High Throughput Analysis accessible for all researchers. The session will include a presentation of the CLC Genomics Workbench software.
June 5th • Singapore
Thursday at 3:30 PM
Aspiration Theatre
Biopolis
June 6th • Kuala Lumpur
Friday at 3 PM
University of Malaya
Institute of Biological Sciences
Free access for all. Sign up by sending an e-mail with your name and organization to ngs@clcbio.com
An article in the MIT Technology Review recently made me aware that ZS Genetics has entered the contest for the Archon X price for Genomics (100 human genomes in 10 days).
ZS Genetics are developing a unique approach to DNA sequencing based on electron microscopy of labeled DNA strands. The technology can potentially sequence very long and contiguous strands of DNA (kilo bases) and can therefore deliver haplotype phase data and help to resolve complex repeat regions.
In comparison to other novel DNA sequencing methods it is a static method based on an image of a fully synthesized DNA strand whereas other technologies are based on the recording of the DNA synthesis process as it occurs.
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!
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.
