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MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies

Norling, Martin and Karlsson, Oskar and Gourlé, Hadrien and Bongcam-Rudloff, Erik and Hayer, Juliette (2016). MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies. PloS one. 11:8, 1-15
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Official URL: http://dx.doi.org/10.1371/journal.pone.0160334

Abstract

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.

Authors/Creators:Norling, Martin and Karlsson, Oskar and Gourlé, Hadrien and Bongcam-Rudloff, Erik and Hayer, Juliette
Title:MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies
Series/Journal:PloS one (1932-6203)
Year of publishing :2016
Volume:11
Number:8
Page range:1-15
Number of Pages:15
Publisher:Public Library of Science
ISSN:1932-6203
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610)
Agrovoc terms:bioinformatics, analysis, genetics
Keywords:metagenomics, bioinformatics analysis, genetics
URN:NBN:urn:nbn:se:slu:epsilon-e-4003
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-4003
Additional ID:
Type of IDID
Web of Science (WoS)000381110300041
DOI10.1371/journal.pone.0160334
ID Code:14127
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Biomedical Sciences and Veterinary Public Health
(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:07 Mar 2017 11:31
Metadata Last Modified:07 Mar 2017 11:31

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