Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

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

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

(2016) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

(2016) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

HostPhinder: A Phage Host Prediction Tool

(2016) Julia Villarroel et al.   Viruses-Basel

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

(2016) Nirav Merchant et al.   PLOS BIOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

(2015) Anastasis Oulas et al.   ENVIRONMENTAL MICROBIOLOGY

A century of the phage: past, present and future

(2015) George P. C. Salmond et al.   NATURE REVIEWS MICROBIOLOGY

HMMER web server: 2015 update

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Programming Bacteriophages by Swapping Their Specificity Determinants

(2015) Moran G. Goren et al.   TRENDS IN MICROBIOLOGY

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

(2015) W B Langdon   BioData Mining

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

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

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

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

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A call for standardized classification of metagenome projects

(2010) Natalia Ivanova et al.   ENVIRONMENTAL MICROBIOLOGY

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

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determination of viral production in aquatic sediments using the dilution-based approach

(2009) Antonio Dell'Anno et al.   Nature Protocols

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Prophinder: a computational tool for prophage prediction in prokaryotic genomes

(2008) Gipsi Lima-Mendez et al.   BIOINFORMATICS

Viral communities associated with healthy and bleaching corals

(2008) Kristen L. Marhaver et al.   ENVIRONMENTAL MICROBIOLOGY

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE