Professor E. Virginia Armbrust, one of our collaborators, published an interesting paper on de novo assembly of metagenomes that is worth paying attention to.
Especially those working on SOLiD data can find use in the tools developed by professor Armbrust’s group, even if you are not working directly on metagenomic data. Vaughn Iverson, the first author of the paper, is a very bright bioinformatician, and he found the standard Velvet assembly program to be of limited use in his analysis. Therefore, he developed a set of custom programs to generate larger scaffolds by connecting and extending contigs generated by Velvet.
Here is the abstract of the paper -
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
Vaughn Iverson, Robert M. Morris, Christian D. Frazar, Chris T. Berthiaume, Rhonda L. Morales, E. Virginia Armbrust
Ecosystems are shaped by complex communities of mostly unculturable microbes. Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain mysterious. To better characterize members of these communities, we developed methods to reconstruct genomes directly from mate-paired short-read metagenomes. We closed a genome representing the as-yet uncultured marine group II Euryarchaeota, assembled de novo from 1.7% of a metagenome sequenced from surface seawater. The genome describes a motile, photo-heterotrophic cell focused on degradation of protein and lipids and clarifies the origin of proteorhodopsin. It also demonstrates that high-coverage mate-paired sequence can overcome assembly difficulties caused by interstrain variation in complex microbial communities, enabling inference of ecosystem functions for uncultured members.