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

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 assemb...

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Published inGenome Biology Vol. 23; no. 1; p. 57
Main Authors Antipov, Dmitry, Rayko, Mikhail, Kolmogorov, Mikhail, Pevzner, Pavel A.
Format Journal Article
LanguageEnglish
Published England BioMed Central 21.02.2022
BMC
Subjects
Assembly
CRISPR sequences
Genome, Bacterial
hosts
Long reads
Metagenome
metagenomics
Metagenomics - methods
prediction
sampling
Sequence Analysis, DNA - methods
Software
viral genome
virus assembly
Virus detection
viruses
Viruses - genetics
Long reads
Assembly
Virus detection
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Summary: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.
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content type line 23
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-021-02566-x