Ray Meta: scalable de novo metagenome assembly and profiling

Genome Biology

Jacques Corbeil²  François Laviolette¹  Élénie Godzaridis³  Frédéric Raymond³  Sébastien Boisvert³ 

[1] Department of Computer Science and Software Engineering, Faculty of Science and Engineering, Laval University, 1065, av. de la Médecine, Québec (Québec), G1V 0A6, Canada;Department of Molecular Medicine, Faculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, Canada;Faculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, Canada

关键词: distributed;    parallel;    next-generation sequencing;    profiling;    de novo assembly;    scalability;    message passing;    metagenomics;   

Others  :  866941
DOI  :  10.1186/gb-2012-13-12-r122

 received in 2012-08-01, accepted in 2012-12-22,  发布年份 2012

【 摘 要 】

Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net webcite.

【 授权许可】

   
2012 Boisvert et al.; licensee BioMed Central Ltd.

【 图 表 】

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