Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Highly Accessed Method

Ray Meta: scalable de novo metagenome assembly and profiling

Sébastien Boisvert12*, Frédéric Raymond12, Élénie Godzaridis2, François Laviolette3 and Jacques Corbeil14

Author affiliations

1 Infectious Diseases Research Center, CHUQ Research Center, 2705, boul. Laurier, Québec (Québec), G1V 4G2, Canada

2 Faculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, Canada

3 Department of Computer Science and Software Engineering, Faculty of Science and Engineering, Laval University, 1065, av. de la Médecine, Québec (Québec), G1V 0A6, Canada

4 Department of Molecular Medicine, Faculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, Canada

For all author emails, please log on.

Citation and License

Genome Biology 2012, 13:R122  doi:10.1186/gb-2012-13-12-r122

Published: 22 December 2012

Abstract

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.

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