Jarrod Chapman
University of California, Berkeley |
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| University of California, Berkeley |
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JAZZ: A whole genome shotgun assembler
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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.
Jarrod Chapman (1,2), Nik Putnam (1,2), Isaac Ho (1), Dan Rokhsar (1,2,3)
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