virMine: automated detection of viral sequences from complex metagenomic samples

PeerJ

article

Andrea Garretto¹  Thomas Hatzopoulos²  Catherine Putonti¹ 

[1] Bioinformatics Program, Loyola University of Chicago;Department of Computer Science, Loyola University of Chicago;Department of Biology, Loyola University of Chicago;Department of Microbiology and Immunology, Loyola University of Chicago

关键词: Virome;    Metagenomics;    Bacteriophage;    Human microbiome;    Freshwater virome;   

DOI  :  10.7717/peerj.6695

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.

【 授权许可】

CC BY