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      Ray Meta: scalable de novo metagenome assembly and profiling

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          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.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2001)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Community structure and metabolism through reconstruction of microbial genomes from the environment.

            Gene W. Tyson, Jarrod Chapman, Philip Hugenholtz … (2004)
            Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
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              Comparative metagenomics of microbial communities.

              Susannah Tringe, Christian von Mering, Arthur Kobayashi … (2005)
              The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.
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                Author and article information

                Contributors
                Sébastien Boisvert
                Frédéric Raymond
                Élénie Godzaridis
                François Laviolette
                Jacques Corbeil
                Journal
                Journal ID (nlm-ta): Genome Biol
                Journal ID (iso-abbrev): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2012
                Publication date (Electronic): 22 December 2012
                Volume: 13
                Issue: 12
                Page: R122
                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
                Article
                Publisher ID: gb-2012-13-12-r122
                DOI: 10.1186/gb-2012-13-12-r122
                PMC ID: 4056372
                PubMed ID: 23259615
                SO-VID: e086281b-aceb-4df6-a3b0-f935a3796f31
                Copyright statement: Copyright © 2012 Boisvert et al.; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 1 August 2012
                Date revision received : 19 November 2012
                Date accepted : 22 December 2012
                Product
                Self URI: http://genomebiology.com/2012/13/12/R122
                Categories
                Subject: Method

                ScienceOpen disciplines: Genetics
                Keywords: metagenomics,message passing,scalability,de novo assembly,profiling,next-generation sequencing,parallel,distributed
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: metagenomics, message passing, scalability, de novo assembly, profiling, next-generation sequencing, parallel, distributed

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