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viralFlye : assembling viruses and identifying their hosts from long-read metagenomics data. / Antipov, Dmitry ; Rayko, Mikhail; Kolmogorov, Mikhail; Pevzner, Pavel A.

In: Genome Biology, Vol. 23, No. 1, 57, 12.2022.

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

BibTeX

@article{8097484157624a35804f62e4d2fdb30f,

title = "viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data",

abstract = "Although the use of long-read sequencing improves the contiguity of assembled viral genomes compared to short-read methods, assembling complex viral communities remains an open problem. We describe the viralFlye tool for identification and analysis of metagenome-assembled viruses in long-read assemblies. We show it significantly improves viral assemblies and demonstrate that long-reads result in a much larger array of predicted virus-host associations as compared to short-read assemblies. We demonstrate that the identification of novel CRISPR arrays in bacterial genomes from a newly assembled metagenomic sample provides information for predicting novel hosts for novel viruses.",

keywords = "Assembly, Long reads, Virus detection, Genome, Bacterial, Metagenome, Viruses/genetics, Metagenomics/methods, Sequence Analysis, DNA/methods",

author = "Dmitry Antipov and Mikhail Rayko and Mikhail Kolmogorov and Pevzner, {Pavel A.}",

note = "Publisher Copyright: {\textcopyright} 2021, The Author(s).",

year = "2022",

month = dec,

doi = "10.1186/s13059-021-02566-x",

language = "English",

volume = "23",

journal = "Genome Biology",

issn = "1474-7596",

publisher = "BioMed Central Ltd.",

number = "1",

}

RIS

TY - JOUR

T1 - viralFlye

T2 - assembling viruses and identifying their hosts from long-read metagenomics data

AU - Antipov, Dmitry

AU - Rayko, Mikhail

AU - Kolmogorov, Mikhail

AU - Pevzner, Pavel A.

PY - 2022/12

Y1 - 2022/12

N2 - Although the use of long-read sequencing improves the contiguity of assembled viral genomes compared to short-read methods, assembling complex viral communities remains an open problem. We describe the viralFlye tool for identification and analysis of metagenome-assembled viruses in long-read assemblies. We show it significantly improves viral assemblies and demonstrate that long-reads result in a much larger array of predicted virus-host associations as compared to short-read assemblies. We demonstrate that the identification of novel CRISPR arrays in bacterial genomes from a newly assembled metagenomic sample provides information for predicting novel hosts for novel viruses.

AB - Although the use of long-read sequencing improves the contiguity of assembled viral genomes compared to short-read methods, assembling complex viral communities remains an open problem. We describe the viralFlye tool for identification and analysis of metagenome-assembled viruses in long-read assemblies. We show it significantly improves viral assemblies and demonstrate that long-reads result in a much larger array of predicted virus-host associations as compared to short-read assemblies. We demonstrate that the identification of novel CRISPR arrays in bacterial genomes from a newly assembled metagenomic sample provides information for predicting novel hosts for novel viruses.

KW - Assembly

KW - Long reads

KW - Virus detection

KW - Genome, Bacterial

KW - Metagenome

KW - Viruses/genetics

KW - Metagenomics/methods

KW - Sequence Analysis, DNA/methods

UR - http://www.scopus.com/inward/record.url?scp=85125155535&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/5f7786cb-ec48-3e77-a576-3f9f41d6838e/

U2 - 10.1186/s13059-021-02566-x

DO - 10.1186/s13059-021-02566-x

M3 - Article

C2 - 35189932

AN - SCOPUS:85125155535

VL - 23

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 1

M1 - 57

ER -

ID: 98422867

viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data

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