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MetLab: An In Silic...
MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies
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- Karlsson Lindsjö, Oskar (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Inst för biomedicin och veterinär folkhälsovetenskap,Department of Animal Breeding and Genetics,Department of Biomedical Science and Veterinary Public Health,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.
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- Gourlé, Hadrien (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet HGEN, SLU Global Bioinformat Ctr, Uppsala, Sweden.
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- Bongcam Rudloff, Erik (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet HGEN, SLU Global Bioinformat Ctr, Uppsala, Sweden.
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- Hayer, Juliette (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet HGEN, SLU Global Bioinformat Ctr, Uppsala, Sweden.
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- Norling, Martin (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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(creator_code:org_t)
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- 2016-08-01
- 2016
- English.
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11
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Abstract
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- LANTBRUKSVETENSKAPER -- Bioteknologi med applikationer på växter och djur -- Genetik och förädling inom lantbruksvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agricultural Biotechnology -- Genetics and Breeding in Agricultural Sciences (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
Publication and Content Type
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- art (subject category)
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