TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data

De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding

(2018) Jiao Chen et al.   BIOINFORMATICS

A Survey of Virus Recombination Uncovers Canonical Features of Artificial Chimeras Generated During Deep Sequencing Library Preparation

(2018) Jean Peccoud et al.   G3-Genes Genomes Genetics

Overview of Virus Metagenomic Classification Methods and Their Biological Applications

(2018) Sam Nooij et al.   Frontiers in Microbiology

De novo assembly of viral quasispecies using overlap graphs

(2017) Jasmijn A. Baaijens et al.   GENOME RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

(2017) David Paez-Espino et al.   Nature Protocols

drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes

(2017) Hsin-Hung Lin et al.   GigaScience

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

(2017) Natalya Yutin et al.   Nature Microbiology

ViromeScan: a new tool for metagenomic viral community profiling

(2016) Simone Rampelli et al.   BMC GENOMICS

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

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

(2016) Yang Li et al.   Scientific Reports

Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data

(2015) Amin Allam et al.   BIOINFORMATICS

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

Virome analysis of antiretroviral-treated HIV patients shows no correlation between T-cell activation and anelloviruses levels

(2015) Linlin Li et al.   JOURNAL OF CLINICAL VIROLOGY

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management

(2015) Mark E. J. Woolhouse et al.   Science Translational Medicine

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing

(2014) Duleepa Jayasundara et al.   BIOINFORMATICS

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

(2014) Simon Roux et al.   BMC BIOINFORMATICS

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research

(2014) Deepak Sharma et al.   JOURNAL OF VIROLOGY

Viral Quasispecies Assembly via Maximal Clique Enumeration

(2014) Armin Töpfer et al.   PLoS Computational Biology

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

(2013) J. Graham Ruby et al.   G3-Genes Genomes Genetics

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Readjoiner: a fast and memory efficient string graph-based sequence assembler

(2012) Giorgio Gonnella et al.   BMC BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Quasispecies dynamics with network constraints

(2012) Valmir C. Barbosa et al.   JOURNAL OF THEORETICAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

ViPR: an open bioinformatics database and analysis resource for virology research

(2011) Brett E. Pickett et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS