Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

Errors in long-read assemblies can critically affect protein prediction

(2019) Mick Watson et al.   NATURE BIOTECHNOLOGY

Reply to ‘Errors in long-read assemblies can critically affect protein prediction’

(2019) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

The ‘Neglected’ Soil Virome – Potential Role and Impact

(2018) Akbar Adjie Pratama et al.   TRENDS IN MICROBIOLOGY

A comprehensive and quantitative exploration of thousands of viral genomes

(2018) Gita Mahmoudabadi et al.   eLife

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

(2018) Saima Sultana Tithi et al.   PeerJ

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean

(2018) Francisco Martinez-Hernandez et al.   ISME Journal

Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome

(2018) Matthew W. Keller et al.   Scientific Reports

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Clinical and biological insights from viral genome sequencing

(2017) Charlotte J. Houldcroft et al.   NATURE REVIEWS MICROBIOLOGY

Ménage à trois in the human gut: interactions between host, bacteria and phages

(2017) Mohammadali Khan Mirzaei et al.   NATURE REVIEWS MICROBIOLOGY

Origins and challenges of viral dark matter

(2017) Siddharth R. Krishnamurthy et al.   VIRUS RESEARCH

Bacteriophage Distributions and Temporal Variability in the Ocean’s Interior

(2017) Elaine Luo et al.   mBio

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

(2017) Francisco Martinez-Hernandez et al.   Nature Communications

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

(2017) Connor B. Driscoll et al.   Standards in Genomic Sciences

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Viral communities of the human gut: metagenomic analysis of composition and dynamics

(2017) Varun Aggarwala et al.   Mobile DNA

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

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

(2016) Nathan A. Ahlgren et al.   NUCLEIC ACIDS RESEARCH

Genomes of Abundant and Widespread Viruses from the Deep Ocean

(2016) Carolina Megumi Mizuno et al.   mBio

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

(2016) J. A. Frank et al.   Scientific Reports

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

(2016) Nirav Merchant et al.   PLOS BIOLOGY

Phage on tap–a quick and efficient protocol for the preparation of bacteriophage laboratory stocks

(2016) Natasha Bonilla et al.   PeerJ

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

(2016) Simon Roux et al.   PeerJ

Pitfalls of haplotype phasing from amplicon-based long-read sequencing

(2016) Thomas W. Laver et al.   Scientific Reports

An Inexpensive, Accurate, and Precise Wet-Mount Method for Enumerating Aquatic Viruses

(2015) Brady R. Cunningham et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Viromes, Not Gene Markers, for Studying Double-Stranded DNA Virus Communities

(2014) Matthew B. Sullivan   JOURNAL OF VIROLOGY

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Supersize me: Cronobacter sakazakii phage GAP32

(2014) Reza Abbasifar et al.   VIROLOGY

Evidence for metaviromic islands in marine phages

(2014) Carolina Megumi Mizuno et al.   Frontiers in Microbiology

A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes

(2013) Bhakti Dwivedi et al.   BMC EVOLUTIONARY BIOLOGY

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

(2013) Bonnie L. Hurwitz et al.   PLoS One

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Metagenomics: microbial diversity through a scratched lens

(2012) Ben Temperton et al.   CURRENT OPINION IN MICROBIOLOGY

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

(2012) Bonnie L. Hurwitz et al.   ENVIRONMENTAL MICROBIOLOGY

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

(2012) Melissa B. Duhaime et al.   ENVIRONMENTAL MICROBIOLOGY

The virocell concept and environmental microbiology

(2012) Patrick Forterre   ISME Journal

Genome of Klebsiella sp.-Infecting Bacteriophage vB_KleM_RaK2

(2012) E. Simoliunas et al.   JOURNAL OF VIROLOGY

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A simple and efficient method for concentration of ocean viruses by chemical flocculation

(2010) Seth G. John et al.   Environmental Microbiology Reports

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

(2009) Michelle M Meyer et al.   BMC GENOMICS

Seasonality and vertical structure of microbial communities in an ocean gyre

(2009) Alexander H Treusch et al.   ISME Journal

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH