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

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

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Detection of novel viruses in porcine fecal samples from China

(2013) Jie-mei Yu et al.   Virology Journal

Study of the Viral and Microbial Communities Associated With Crohn’s Disease: A Metagenomic Approach

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Estimation of viral richness from shotgun metagenomes using a frequency count approach

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A de novo metagenomic assembly program for shotgun DNA reads

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De novo assembly of highly diverse viral populations

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Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

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A framework for human microbiome research

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

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Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

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Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

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Sequence Analysis of the Human Virome in Febrile and Afebrile Children

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Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

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Metagenomic Exploration of Viruses throughout the Indian Ocean

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Evaluating de Bruijn Graph Assemblers on 454 Transcriptomic Data

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De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

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Evolutionarily Conserved Orthologous Families in Phages Are Relatively Rare in Their Prokaryotic Hosts

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Genovo: De Novo Assembly for Metagenomes

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How environmental solution conditions determine the compaction velocity of single DNA molecules

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Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

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Complete genome sequence of a marine roseophage provides evidence into the evolution of gene transfer agents in alphaproteobacteria

(2011) Sijun Huang et al.   Virology Journal

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

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Role of the gut microbiota in defining human health

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Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

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Metagenomic analysis of the turkey gut RNA virus community

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A Primer on Metagenomics

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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

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Genome assembly reborn: recent computational challenges

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Identification of ORF636 in Phage  SLT Carrying Panton-Valentine Leukocidin Genes, Acting as an Adhesion Protein for a Poly(Glycerophosphate) Chain of Lipoteichoic Acid on the Cell Surface of Staphylococcus aureus

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Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis

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Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

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Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

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Aggressive assembly of pyrosequencing reads with mates

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Innate immunity and intestinal microbiota in the development of Type 1 diabetes

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MetaSim—A Sequencing Simulator for Genomics and Metagenomics

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Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

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Viral diversity and dynamics in an infant gut

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