Metaviral SPAdes: assembly of viruses from metagenomic data

CAMISIM: simulating metagenomes and microbial communities

(2019) Adrian Fritz et al.   Microbiome

Plasmid detection and assembly in genomic and metagenomic datasets

(2019) Dmitry Antipov et al.   GENOME RESEARCH

virMine: automated detection of viral sequences from complex metagenomic samples

(2019) Andrea Garretto et al.   PeerJ

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution

(2018) Jason W. Shapiro et al.   mBio

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Telomeres and viruses: common themes of genome maintenance

(2012) Zhong Deng et al.   Frontiers in Oncology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS