ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis

Genome binning of viral entities from bulk metagenomics data

(2022) Joachim Johansen et al.   Nature Communications

ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

(2022) Alfred Ferrer Florensa et al.   Microbial Genomics

vRhyme enables binning of viral genomes from metagenomes

(2022) Kristopher Kieft et al.   NUCLEIC ACIDS RESEARCH

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

(2022) Ann C. Gregory et al.   Microbiome

Improved metagenome binning and assembly using deep variational autoencoders

(2021) Jakob Nybo Nissen et al.   NATURE BIOTECHNOLOGY

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

(2021) Jiarong Guo et al.   Microbiome

Fast and sensitive taxonomic assignment to metagenomic contigs

(2021) M Mirdita et al.   BIOINFORMATICS

TaxonKit: A practical and efficient NCBI taxonomy toolkit

(2021) Wei Shen et al.   Journal of Genetics and Genomics

BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains

(2021) Adam J. Hockenberry et al.   PeerJ

Simulation study and comparative evaluation of viral contiguous sequence identification tools

(2021) Cody Glickman et al.   BMC BIOINFORMATICS

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

(2021) Akbar Adjie Pratama et al.   PeerJ

Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma

(2021) Tianli Ma et al.   Microorganisms

Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner

(2020) Mohammadali Khan Mirzaei et al.   Cell Host & Microbe

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

(2020) Wenjun Li et al.   NUCLEIC ACIDS RESEARCH

Gut mucosal virome alterations in ulcerative colitis

(2019) Tao Zuo et al.   GUT

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

(2019) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

(2019) Adam G. Clooney et al.   Cell Host & Microbe

OUP accepted manuscript

(2018)   BIOINFORMATICS

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data

(2018) Saima Sultana Tithi et al.   PeerJ

A human gut phage catalog correlates the gut phageome with type 2 diabetes

(2018) Yingfei Ma et al.   Microbiome

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

VFDB 2019: a comparative pathogenomic platform with an interactive web interface

(2018) Bo Liu et al.   NUCLEIC ACIDS RESEARCH

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

VirusSeeker, a computational pipeline for virus discovery and virome composition analysis

(2017) Guoyan Zhao et al.   VIROLOGY

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

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

(2017) Simon Roux et al.   PeerJ

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

ViromeScan: a new tool for metagenomic viral community profiling

(2016) Simone Rampelli et al.   BMC GENOMICS

VIP: an integrated pipeline for metagenomics of virus identification and discovery

(2016) Yang Li et al.   Scientific Reports

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metavir: a web server dedicated to virome analysis

(2011) Simon Roux et al.   BIOINFORMATICS

TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

(2011) Hernan A. Lorenzi et al.   Standards in Genomic Sciences

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Quick Guide to Organizing Computational Biology Projects

(2009) William Stafford Noble   PLoS Computational Biology