JAZZ: A whole genome shotgun assembler

Jarrod Chapman, University of California, Berkeley

We have implemented a new graphical algorithm (JAZZ) for self-consistently reconstructing large genomes from paired-end shotgun sequence data. The system was designed and parallelized for application to genomes of hundred-megabase to gigabase scale. To aid in the evaluation of the assembly process we have also created a suite of tools for visualization and analysis of large assemblies and WGS data sets. Here I present a broad overview of the assembly process, its computational challenges, and results for several genome projects including the sea squirt  Ciona intestinalis and the Japanese pufferfish Fugu rubripes.

Abstract Author(s): Jarrod Chapman (1,2), Nik Putnam (1,2), Isaac Ho (1), Dan Rokhsar (1,2,3)