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.
Via GenomeWeb, I had quite a laugh at Keith Robinson’s recent blog post on Metagenomic Analysis with Galaxy: Windshield Genomics and Beyond - a dataset he came across while browsing the NCBI Short Read Archive, with the following abstract:
When I drive through Pennsylvania in June my windshield gets quite dirty with all these bugs. Yet do I know what they are? How many beetles versus butterflies? Is there a difference between day and night? Is there a difference between Pennsylvania and Connecticut? So we scraped the windshield, isolated genomic DNA, and subjected it to 454 FLX sequencing. We then uploaded the data into Galaxy and attempted answering these questions. In the end Pennsylvania turned out to be different from Connecticut.
It’s certainly an alternative use of high-throughput sequencing capacity at this point, but a fun one!
On a related note I might add that I would like to read a physics article on windshield dynamics, as I - through ongoing empirical observations - experience a dramatical increase in the number of bugs squashed on my windshield if my average commuting speed is raised by around 10%…
