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METAVIRALSPADES : assembly of viruses from metagenomic data. / Antipov, Dmitry; Raiko, Mikhail; Lapidus, Alla; Pevzner, Pavel A.

In: Bioinformatics, Vol. 36, No. 14, 15.07.2020, p. 4126-4129.

Research output: Contribution to journal › Article › peer-review

Harvard

Antipov, D, Raiko, M, Lapidus, A & Pevzner, PA 2020, 'METAVIRALSPADES: assembly of viruses from metagenomic data', Bioinformatics, vol. 36, no. 14, pp. 4126-4129. https://doi.org/10.1093/bioinformatics/btaa490, https://doi.org/10.1093/bioinformatics/btaa490, https://doi.org/10.1093/bioinformatics/btaa490

APA

Antipov, D., Raiko, M., Lapidus, A., & Pevzner, P. A. (2020). METAVIRALSPADES: assembly of viruses from metagenomic data. Bioinformatics, 36(14), 4126-4129. https://doi.org/10.1093/bioinformatics/btaa490, https://doi.org/10.1093/bioinformatics/btaa490, https://doi.org/10.1093/bioinformatics/btaa490

Vancouver

Antipov D, Raiko M, Lapidus A, Pevzner PA. METAVIRALSPADES: assembly of viruses from metagenomic data. Bioinformatics. 2020 Jul 15;36(14):4126-4129. https://doi.org/10.1093/bioinformatics/btaa490, https://doi.org/10.1093/bioinformatics/btaa490, https://doi.org/10.1093/bioinformatics/btaa490

Author

Antipov, Dmitry ; Raiko, Mikhail ; Lapidus, Alla ; Pevzner, Pavel A. / METAVIRALSPADES : assembly of viruses from metagenomic data. In: Bioinformatics. 2020 ; Vol. 36, No. 14. pp. 4126-4129.

BibTeX

@article{3393480eff97416080ff54ccdc7eebe9,
title = "METAVIRALSPADES: assembly of viruses from metagenomic data",
abstract = "Motivation: Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth's virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies.Results: We describe a METAVIRALSPADES tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked METAVIRALSPADES on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models and demonstrated that it improves on the state-of-the-art viral identification pipelines.",
author = "Dmitry Antipov and Mikhail Raiko and Alla Lapidus and Pevzner, {Pavel A.}",
note = "Publisher Copyright: {\textcopyright} The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. Copyright: This record is sourced from MEDLINE/PubMed, a database of the U.S. National Library of Medicine",
year = "2020",
month = jul,
day = "15",
doi = "10.1093/bioinformatics/btaa490",
language = "English",
volume = "36",
pages = "4126--4129",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "14",

}

RIS

TY - JOUR

T1 - METAVIRALSPADES

T2 - assembly of viruses from metagenomic data

AU - Antipov, Dmitry

AU - Raiko, Mikhail

AU - Lapidus, Alla

AU - Pevzner, Pavel A.

N1 - Publisher Copyright: © The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. Copyright: This record is sourced from MEDLINE/PubMed, a database of the U.S. National Library of Medicine

PY - 2020/7/15

Y1 - 2020/7/15

N2 - Motivation: Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth's virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies.Results: We describe a METAVIRALSPADES tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked METAVIRALSPADES on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models and demonstrated that it improves on the state-of-the-art viral identification pipelines.

AB - Motivation: Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth's virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies.Results: We describe a METAVIRALSPADES tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked METAVIRALSPADES on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models and demonstrated that it improves on the state-of-the-art viral identification pipelines.

UR - https://www.mendeley.com/catalogue/41952930-6b5d-3681-824f-58b4ce685f41/

UR - http://www.scopus.com/inward/record.url?scp=85088881608&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btaa490

DO - 10.1093/bioinformatics/btaa490

M3 - Article

VL - 36

SP - 4126

EP - 4129

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 14

ER -

ID: 60527501