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Ray Meta: scalable de novo metagenome assembly and profiling.

作者信息

Boisvert Sébastien, Raymond Frédéric, Godzaridis Elénie, Laviolette François, Corbeil Jacques

出版信息

Genome Biol. 2012 Dec 22;13(12):R122. doi: 10.1186/gb-2012-13-12-r122.


DOI:10.1186/gb-2012-13-12-r122
PMID:23259615
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4056372/
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.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/cca249767a03/gb-2012-13-12-r122-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/46a07fa1494c/gb-2012-13-12-r122-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/5c9a46f71b17/gb-2012-13-12-r122-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/c777e3dd4adc/gb-2012-13-12-r122-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/58c4ad92491e/gb-2012-13-12-r122-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/cca249767a03/gb-2012-13-12-r122-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/46a07fa1494c/gb-2012-13-12-r122-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/5c9a46f71b17/gb-2012-13-12-r122-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/c777e3dd4adc/gb-2012-13-12-r122-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/58c4ad92491e/gb-2012-13-12-r122-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1c8/4056372/cca249767a03/gb-2012-13-12-r122-5.jpg

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本文引用的文献

[1]
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.

Nucleic Acids Res. 2012-7-19

[2]
Structure, function and diversity of the healthy human microbiome.

Nature. 2012-6-13

[3]
Metagenomic microbial community profiling using unique clade-specific marker genes.

Nat Methods. 2012-6-10

[4]
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Nat Rev Genet. 2012-3-13

[5]
De novo assembly and genotyping of variants using colored de Bruijn graphs.

Nat Genet. 2012-1-8

[6]
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.

Curr Opin Biotechnol. 2011-12-9

[7]
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

ISME J. 2011-12-1

[8]
Repetitive DNA and next-generation sequencing: computational challenges and solutions.

Nat Rev Genet. 2011-11-29

[9]
Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the High Arctic.

Appl Environ Microbiol. 2011-11-11

[10]
How to apply de Bruijn graphs to genome assembly.

Nat Biotechnol. 2011-11-8

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