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
[Journal article]
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Available under License Creative Commons Attribution. 999kB |
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 | ||||||
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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 | ||||||
Copyright: | Creative Commons: Attribution 4.0 | ||||||
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: |
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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: | 24 Oct 2020 20:26 |
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