Parallel Genome Assembly

Recent advances in genome assembly technology have made short-read sequencing a promising and relatively inexpensive alternative to the more traditional approaches. However, the amount of data generated by these de novo approaches can be orders of magnitude larger than that assembled by previous generation sequencers. The primary goal of the project is to enable very large-scale genome assembly on highly parallel computer architectures. The anticipated product will be a fully scalable, extensible and re-usable toolkit implementing all of the functions required to build and manipulate de Bruijn graphs of a size limited only by available hardware. As a demonstration of the capabilities of the toolkit, a fully functional genome assembler will be produced.

Investigators: Victor Jongeneel, Jian Ma, Laxmikant V. Kale