Journal
GENOME BIOLOGY
Volume 13, Issue 12, Pages -Publisher
BMC
DOI: 10.1186/gb-2012-13-12-r122
Keywords
metagenomics; message passing; scalability; de novo assembly; profiling; next-generation sequencing; parallel; distributed
Funding
- Canada Foundation for Innovation (CFI)
- National Science and Engineering Research Council (NSERC)
- NanoQuebec
- Fonds Quebecois de Recherche sur la Nature et les Technologies (FQRNT)
- Canadian Institutes for Health Research (CIHR) [200910GSD 226209 172830]
- Fonds de recherche du Quebec - Nature et technologies [2013-PR-166708]
- Natural Sciences and Engineering Research Council of Canada [262067]
- Consortium Quebecois sur la decouverte du medicament (CQDM)
- Mitacs through the Mitacs-Accelerate program
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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.
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