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

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

(2017) John Vollmers et al.   PLoS One

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

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

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

(2017) Benjamin Bolduc et al.   PeerJ

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

(2016) Ann C. Gregory et al.   BMC GENOMICS

The bright side of microbial dark matter: lessons learned from the uncultivated majority

(2016) Lindsey Solden et al.   CURRENT OPINION IN MICROBIOLOGY

Genomic diversification of marine cyanophages into stable ecotypes

(2016) Marcia F. Marston et al.   ENVIRONMENTAL MICROBIOLOGY

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

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

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

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

(2016) Simon Roux et al.   PeerJ

Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Where Next for Microbiome Research?

(2015) Matthew K. Waldor et al.   PLOS BIOLOGY

Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

(2015) Ramy K. Aziz et al.   Frontiers in Microbiology

Omega: an Overlap-graph de novo Assembler for Metagenomics

(2014) Bahlul Haider et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Evaluation of viral genome assembly and diversity estimation in deep metagenomes

(2014) Daniel Aguirre de Cárcer et al.   BMC GENOMICS

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut

(2014) Jorge F Vázquez-Castellanos et al.   BMC GENOMICS

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

Unveiling viral–host interactions within the ‘microbial dark matter’

(2014) Manuel Martínez-García et al.   Nature Communications

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

(2013) Hannah M Doll et al.   BMC MICROBIOLOGY

Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses

(2013) Elke Allers et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

NeSSM: A Next-Generation Sequencing Simulator for Metagenomics

(2013) Ben Jia et al.   PLoS One

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

Seasonality and monthly dynamics of marine myovirus communities

(2012) Cheryl-Emiliane T. Chow 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

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Are we missing half of the viruses in the ocean?

(2012) Grieg F Steward et al.   ISME Journal

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

(2012) Simon Roux et al.   PLoS One

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Development ofphoHas a Novel Signature Gene for Assessing Marine Phage Diversity

(2011) Dawn B. Goldsmith et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

(2011) A. D. Tadmor et al.   SCIENCE

Microbes do not follow the elevational diversity patterns of plants and animals

(2010) Noah Fierer et al.   ECOLOGY

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Recombination and microdiversity in coastal marine cyanophages

(2009) Marcia F. Marston et al.   ENVIRONMENTAL MICROBIOLOGY

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

(2009) Florent E. Angly et al.   PLoS Computational Biology

Assembly of Viral Metagenomes from Yellowstone Hot Springs

(2008) T. Schoenfeld et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Distantly sampled soils carry few species in common

(2008) Roberta R Fulthorpe et al.   ISME Journal

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE