Next Generation Sequencing

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.