Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

(2011) Dongying Wu et al.   PLoS One

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

(2011) Miguel Pignatelli et al.   PLoS One

SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1.

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics

(2010) Johannes Goll et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

(2009) J. Muller et al.   NUCLEIC ACIDS RESEARCH

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Discovering Functional Novelty in Metagenomes: Examples from Light-Mediated Processes

(2008) A. H. Singh et al.   JOURNAL OF BACTERIOLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Molecular eco-systems biology: towards an understanding of community function

(2008) Jeroen Raes et al.   NATURE REVIEWS MICROBIOLOGY

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

(2008) D. Chivian et al.   SCIENCE