Ray Meta: scalable de novo metagenome assembly and profiling

被引：414

作者：

Boisvert, Sebastien ^{[1
,2
]}

Raymond, Frederic ^{[1
,2
]}

Godzaridis, Elenie ^{[2
]}

Laviolette, Francois ^{[3
]}

Corbeil, Jacques ^{[1
,4
]}

机构：

[1] CHUQ Res Ctr, Infect Dis Res Ctr, Quebec City, PQ G1V 4G2, Canada

[2] Univ Laval, Fac Med, Quebec City, PQ G1V 0A6, Canada

[3] Univ Laval, Dept Comp Sci & Software Engn, Fac Sci & Engn, Quebec City, PQ G1V 0A6, Canada

[4] Univ Laval, Dept Mol Med, Fac Med, Quebec City, PQ G1V 0A6, Canada

来源：

GENOME BIOLOGY | 2012年 / 13卷 / 12期

基金：

加拿大自然科学与工程研究理事会; 加拿大创新基金会;

关键词：

metagenomics; message passing; scalability; de novo assembly; profiling; next-generation sequencing; parallel; distributed; MICROBIAL MAT COMMUNITIES; PHYLOGENETIC CLASSIFICATION; GENE ONTOLOGY; DNA; SEQUENCES; GENOMES;

D O I：

10.1186/gb-2012-13-12-r122

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

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.

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页数：13

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