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

Mikhail Kolmogorov,Mikhail Rayko,Pavel A. Pevzner,Dmitry Antipov

doi:10.1186/s13059-021-02566-x

Mikhail Kolmogorov, Mikhail Rayko + Show 2 more

Open Access

https://doi.org/10.1186/s13059-021-02566-x

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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.

Highlights

Various metagenomic studies have greatly expanded the set of known viral genomes [1,2,3,4,5,6] and have raised the challenge of inferring the metagenome-assembled viruses (MAVs)
Short-read sequencing has been the dominant technology for the discovery of novel MAVs [2]
We show that long reads improve the accuracy of virus-host association predictions based on matching of the CRISPR-Cas sites

Summary

Introduction

Various metagenomic studies have greatly expanded the set of known viral genomes [1,2,3,4,5,6] and have raised the challenge of inferring the metagenome-assembled viruses (MAVs). Since the International Committee on Taxonomy of Viruses has proposed to include MAVs into viral taxonomy studies [7], there is a need for novel bioinformatics tools to accurately assemble, identify, verify, analyze, and classify MAVs. So far, short-read sequencing has been the dominant technology for the discovery of novel MAVs [2]. Short-read sequencing has been the dominant technology for the discovery of novel MAVs [2] Such discoveries are usually conducted by assembling a viral metagenome (virome) using general-purpose metagenomic assemblers (such as metaSPAdes [8] or Megahit [9]), or specialized viral assemblers (such as metaviralSPAdes [10]). Complete sequencing of giant viruses has been a challenging task [12, 13]

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