SC12 Home > SC12 Schedule > SC12 Presentation - An Ultra-Fast Computing Pipeline for Metagenome Analysis with Next-Generation DNA Sequencers

SCHEDULE: NOV 10-16, 2012

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An Ultra-Fast Computing Pipeline for Metagenome Analysis with Next-Generation DNA Sequencers

SESSION: ACM Student Research Competition Poster Session

EVENT TYPE: ACM Student Research Competition

TIME: 5:15PM - 7:00PM

SESSION CHAIR: Torsten Hoefler

AUTHOR(S):Shuji Suzuki

ROOM:East Entrance

Metagenome analysis is useful for not only understanding symbiotic systems but also watching environment pollutions. However, metagenome analysis requires sensitive sequence homology searches which require large computation time and it is thus a bottleneck in current metagenome analysis based on the data from the latest DNA sequencers generally called a next-generation sequencer (NGS). To solve the problem, we developed a new efficient GPU-based homology search program GHOSTM and a large-scale automated computing pipeline for analyzing huge amount of metagenomic data obtained from a NGS. This pipeline enables us to analyze metagenomic data from a NGS in real time by utilizing huge computational resources on TSUBAME2. For homology search, the pipeline can utilize both GHOSTM and BLASTX, which has been generally used for previous metagenomic researches. By using the new program and pipeline, we achieved to process metagenome information obtained from a single run of a NGS in a few hours.

Chair/Author Details:

Torsten Hoefler (Chair) - ETH Zurich

Shuji Suzuki - Tokyo Institute of Technology

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