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
Helicos Biosciences have announced a partnership with the Children’s Oncology Group (COG) where Helicos will use their NGS platform to experimentally characterize different tissue types from patients with Ewing’s sarcoma, a rare cancer.
In their press release they state that:
These samples include a normal bone marrow sample and tumor cell lines derived from a Ewing’s sarcoma primary tumor biopsy and the metastasis from the same patient obtained after two cycles of chemotherapy. It is hoped that an in-depth comparison of genomic DNA sequence and RNA expression between the normal tissue, primary tumor, and treatment resistant metastasis will reveal structural and functional genomic changes associated with clinical aggressiveness and treatment resistance.
The study will include an ambitious range of applications for NGS technology as it will aim to identify rare mutations, polymorphisms, copy number variants, true whole-genome RNA transcriptional activity, and global methylation patterns.
The press release does not mention anything about the tissue sample sizes that will be collected as starting material, so I guess I will have to read the papers at some point 
. However, the ability to characterize very small tissue samples is one of the most interesting features of the single molecule sequencing technologies, so it will be interesting to see how the technology performs for this type of problems.
PolITiGenomics have posted some details about the upcoming update to the 454 system.
According to the blog, the next upgrade will be called Titanium and will have twice the number of cycles increasing the average read length from 250 to around 400 bases. Furthermore, the new version will have smaller, more densely packed wells on the picotiter plate which will increases the number of DNA fragments sequenced per run. All together, 454 FLX Titanium runs will quintuple their data output from 100 Mb to about 500 Mb.
Obviously, the increased data amount will put even more strain on the downstream image- and sequence analyses pipelines.
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
