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

↓ Direkt till sidans innehåll
↓ Direkt till sidans sekundära innehåll (sidomenyn)

Search: onr:"swepub:oai:slubar.slu.se:77063" > MetLab: An In Silic...

1 of 1
Previous record
Next record
To hitlist

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

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.

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.

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.

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.

Norling, Martin (author): Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi

show less...

(creator_code:org_t)

2016-08-01
2016
English.
In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11

Related links:: https://pub.epsilon.... (primary) (Raw object) (free); show more...; https://journals.plo...; https://doi.org/10.1...; https://uu.diva-port... (primary) (Raw object); https://res.slu.se/i...; https://doi.org/10.1...; https://urn.kb.se/re...; show less...

Journal article (peer-reviewed)

Abstract Subject headings

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.

Find in a library

PLoS ONE (Search for host publication in LIBRIS)

To the university's database

1 of 1
Previous record
Next record
To hitlist

Find more in SwePub

By the author/editor: Karlsson Lindsjö ...; Gourlé, Hadrien; Bongcam Rudloff, ...; Hayer, Juliette; Norling, Martin

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

AGRICULTURAL SCIENCES: AGRICULTURAL SCI ...; and Agricultural Bio ...; and Genetics and Bre ...

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Bioinformatics

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...

Articles in the publication: PLoS ONE

By the university: Swedish University of Agricultural Sciences; Uppsala University

Search outside SwePub

Extend your search to:: Google; Google Book Search; Google Scholar

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

LIBRIS.kb.se

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

Subject headings

Publication and Content Type

Find in a library

To the university's database

Find more in SwePub

Search outside SwePub