Next Generation Sequencing

You can find the answer to this question as well as other interesting facts about us and our customers and partners - all written in a very nice article by Editor-in-Chief, Kevin Davies, in the newest edition of Bio-IT World’s Magazine.

Click to read “CLC bio Satisfies Next-Gen Bioinformatics Cravings”

At ISMB in Stockholm, July 2009, Bujie Zhan et al. of Department of Genetics and Biotechnology at Aarhus University, published a poster where they have compared various de novo assembly algorithms to see which one delivered the best results to outline the most efficient de novo assembly strategy for bacterial genomes.

CLC bio’s de novo assembly algorithm was compared to edena, SSAKE, Velvet, and 454’s Newbler, and was found to give the largest contig size with Solexa data. The performance of CLC bio’s assembler was especially good, when doing hybrid assemblies of data from both 454 and Solexa instruments.

Click here to download the “Comparison of assembly strategies for high-throughput de novo sequencing of bacterial genomes” poster (80 KB) in PDF format.

This Monday, Stephen Quake et al. published an article in Nature Biotechnology on the first human genome sequenced with a Single-Molecule Sequencing approach using Helicos’ platform.

The publication has garnered quite an amount of PR, being cited in both New York Times and The Independent, while the scientific community has blogged and twitted extensively on the subject.

We have assembled a small collection of links on the subject that are definitely worth reading!

Bio-IT World:
Quake Sequences Personal Genome Using Helicos Single-Molecule Sequencing
The Single Life: Stephen Quake Q&A

Time Online:
Inflated claims for the $50,000 genome

Ed Yong at his Not Exactly Rocket Science blog wrote…

Julie Dunning-Hotopp from the J. Craig Venter Institute and Michael Clark from the University of Rochester have found a drastic strategy used by Wolbachia to preserve its own immortality - inserting its entire genome wholesale into that of another living thing.

Click here to read the exciting article.

Last week Nicola Palmieri and Christian Schlötterer of Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Vienna, Austria, published an article in PLoS ONE, Vol. 4, No. 7. (28 July 2009), e6323, under the headline Mapping Accuracy of Short Reads from Massively Parallel Sequencing and the Implications for Quantitative Expression Profiling.

This is the conclusions of the article:

In complex genomes, expression profiling by massively parallel sequencing could introduce a considerable bias due to incorrectly mapped sequence reads if the read length is short. Nevertheless, this bias could be accounted for if the genomic sequence is known. Furthermore, sequence polymorphisms and indels also affect the mapping accuracy and may cause a biased gene expression measurement. The choice of the mapping software is highly critical and the reliability depends on the presence/absence of indels and the divergence between reads and the reference genome. Overall, we found SSAHA2 and CLC to produce the most reliable mapping results.

We’re of course very happy to see our own internal findings confirmed in an independent study, even though they only had our command-line application CLC NGS Cell running at fraction of the speed it’s capable of - and still retain full quality.