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MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet HGEN, SLU Global Bioinformat Ctr, Uppsala, Sweden.;Swedish Univ Agr Sci SLU, Dept Biomed Sci & Vet Publ Hlth BVF, Uppsala, Sweden.;OIE Collaborating Ctr Biotechnol Based Diag Infec, Uppsala, Sweden..
Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet HGEN, SLU Global Bioinformat Ctr, Uppsala, Sweden..
Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet HGEN, SLU Global Bioinformat Ctr, Uppsala, Sweden..
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2016 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 8, e0160334Article in journal (Refereed) Published
Abstract [en]

Metagenomics, the sequence characterization of all genomes within a sample, is widely used as a virus discovery tool as well as a tool to study viral diversity of animals. Metagenomics can be considered to have three main steps; sample collection and preparation, sequencing and finally bioinformatics. Bioinformatic analysis of metagenomic datasets is in itself a complex process, involving few standardized methodologies, thereby hampering comparison of metagenomics studies between research groups. In this publication the new bioinformatics framework MetLab is presented, aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes. MetLab provides support in designing the metagenomics experiment by estimating the sequencing depth needed for the complete coverage of a species. This is achieved by applying a methodology to calculate the probability of coverage using an adaptation of Stevens' theorem. It also provides scientists with several pipelines aimed at simplifying the analysis of viral metagenomes, including; quality control, assembly and taxonomic binning. We also implement a tool for simulating metagenomics datasets from several sequencing platforms. The overall aim is to provide virologists with an easy to use tool for designing, simulating and analyzing viral metagenomes. The results presented here include a benchmark towards other existing software, with emphasis on detection of viruses as well as speed of applications. This is packaged, as comprehensive software, readily available for Linux and OSX users at https://github.com/norling/metlab.

Place, publisher, year, edition, pages
2016. Vol. 11, no 8, e0160334
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-303749DOI: 10.1371/journal.pone.0160334ISI: 000381110300041PubMedID: 27479078OAI: oai:DiVA.org:uu-303749DiVA: diva2:973870
Swedish Research Council Formas, 221-2012-586EU, European Research Council, Home/2009/ISEC/AG/191EU, FP7, Seventh Framework Programme, 612583
Available from: 2016-09-23 Created: 2016-09-23 Last updated: 2016-10-07Bibliographically approved

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