Next Generation Sequencing

No doubt there are some great bioinfomatics challenges in using NGS data. Some of these are summarized in a new Trends in Genetics review by Misha Pop and Steven L. Salzberg.

In the paper Pop and Salzberg are quite pessimistic regarding the use of short read sequences in whole genome assembly. Their pessimism is partially based on the lack of paired-end data from NGS technologies which results in fragmented assemblies.

However, as both 454, Solexa and Solid are currently testing and refining paired-end protocols I think that these challenges are likely to be overcome in the near future. Pop and Salzberg quote several simulation studies of the suitability of short reads for genome assembly but unfortunately there are no simulation studies out using short reads along with paired-end information.