A clinician's guide to microbiome analysis

A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome

(2017) Maria Elisa Perez-Muñoz et al.   Microbiome

Comparison of Collection Methods for Fecal Samples in Microbiome Studies

(2016) Emily Vogtmann et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

DUDes: a top-down taxonomic profiler for metagenomics

(2016) Vitor C. Piro et al.   BIOINFORMATICS

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing

(2016) Laura Becker et al.   Scientific Reports

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome

(2016) Ericka L. Anderson et al.   Scientific Reports

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

The Effects of Bowel Preparation on Microbiota-Related Metrics Differ in Health and in Inflammatory Bowel Disease and for the Mucosal and Luminal Microbiota Compartments

(2016) Rima M Shobar et al.   Clinical and Translational Gastroenterology

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

(2016) Cian J. Hill et al.   Microbiome

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies

(2016) Euan Watt et al.   Microbiome

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room?

(2016) Alexander G. Shaw et al.   Microbiome

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

Open-Source Sequence Clustering Methods Improve the State Of the Art

(2016) Evguenia Kopylova et al.   mSystems

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

(2016) Adam G. Clooney et al.   PLoS One

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

(2016) Hsin-Hung Lin et al.   Scientific Reports

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

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

(2015) Dinghua Li et al.   BIOINFORMATICS

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

(2015) Bruno Fosso et al.   BMC BIOINFORMATICS

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

(2015) Michael A. Peabody et al.   BMC BIOINFORMATICS

SPINGO: a rapid species-classifier for microbial amplicon sequences

(2015) Guy Allard et al.   BMC BIOINFORMATICS

MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes

(2015) Pavel Petrenko et al.   BMC BIOLOGY

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

(2015) Jarmo Ritari et al.   BMC GENOMICS

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Classification of Metagenomics Data at Lower Taxonomic Level Using a Robust Supervised Classifier

(2015) Tao Hou et al.   Evolutionary Bioinformatics

Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences

(2015) Ashok K. Sharma et al.   GENOMICS

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers

(2015) A Lavelle et al.   GUT

MtHc: a motif-based hierarchical method for clustering massive 16S rRNA sequences into OTUs

(2015) Ze-Gang Wei et al.   Molecular BioSystems

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

(2015) Tracey Allen K. Freitas et al.   NUCLEIC ACIDS RESEARCH

Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics

(2015) Brittany Goldberg et al.   mBio

Systems biology of host-microbe metabolomics

(2015) Almut Heinken et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

(2015) Davide Albanese et al.   Scientific Reports

Sample storage conditions significantly influence faecal microbiome profiles

(2015) Jocelyn M Choo et al.   Scientific Reports

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering

(2015) Oscar Franzén et al.   Microbiome

Collection media and delayed freezing effects on microbial composition of human stool

(2015) Roberto Flores et al.   Microbiome

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

(2015) Eugen Bauer et al.   Microbiome

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

(2015) Jake Jervis-Bardy et al.   Microbiome

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets

(2015) Nikhil Chaudhary et al.   PLoS One

Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum

(2015) Rodrick J. Chiodini et al.   PLoS One

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool

(2015) Monika A. Gorzelak et al.   PLoS One

Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing

(2015) Marcia L. Hart et al.   PLoS One

CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies

(2014) Mohamed Mysara et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Omega: an Overlap-graph de novo Assembler for Metagenomics

(2014) Bahlul Haider et al.   BIOINFORMATICS

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

(2014) J. Dröge et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning

(2014) Yi Wang et al.   BMC GENOMICS

Microbes, Microbiota, and Colon Cancer

(2014) Cynthia L. Sears et al.   Cell Host & Microbe

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning

(2014) Afiahayati et al.   DNA RESEARCH

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets

(2014) Rachamalla Maheedhar Reddy et al.   GENOMICS

Metaphor: Finding Bi-directional Best Hit homology relationships in (meta)genomic datasets

(2014) Bernd E. van der Veen et al.   GENOMICS

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification

(2014) David Koslicki et al.   PLoS One

Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization

(2014) Xiaoquan Su et al.   PLoS One

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

Quantifying the Effect of Ribosomal Density on mRNA Stability

(2014) Shlomit Edri et al.   PLoS One

Rectal Swabs for Analysis of the Intestinal Microbiota

(2014) Andries E. Budding et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

(2014) Florent E Angly et al.   Microbiome

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

(2014) Susan M Huse et al.   Microbiome

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

(2014) Agata Wesolowska-Andersen et al.   Microbiome

Meta-QC-Chain: Comprehensive and Fast Quality Control Method for Metagenomic Data

(2014) Qian Zhou et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles

(2013) Michael S. Porter et al.   BIOINFORMATICS

Protein signature-based estimation of metagenomic abundances including all domains of life and viruses

(2013) Heiner Klingenberg et al.   BIOINFORMATICS

FunFrame: functional gene ecological analysis pipeline

(2013) David Weisman et al.   BIOINFORMATICS

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

M-pick, a modularity-based method for OTU picking of 16S rRNA sequences

(2013) Xiaoyu Wang et al.   BMC BIOINFORMATICS

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences

(2013) Christina Ander et al.   BMC BIOINFORMATICS

Gene prediction in metagenomic fragments based on the SVM algorithm

(2013) Yongchu Liu et al.   BMC BIOINFORMATICS

Optimal preservation of liver biopsy samples for downstream translational applications

(2013) Alana R. Sherker et al.   Hepatology International

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Topographic diversity of fungal and bacterial communities in human skin

(2013) Keisha Findley et al.   NATURE

Medicines from microbiota

(2013) Bernat Olle   NATURE BIOTECHNOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Intestinal Microbial Metabolism of Phosphatidylcholine and Cardiovascular Risk

(2013) W.H. Wilson Tang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

(2013) Sarah Hunter et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

(2013) Wei Chen et al.   PLoS One

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

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

(2012) Y. Peng et al.   BIOINFORMATICS

Storage conditions of intestinal microbiota matter in metagenomic analysis

(2012) Silvia Cardona et al.   BMC MICROBIOLOGY

Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

(2012) Martin Iain Bahl et al.   FEMS MICROBIOLOGY LETTERS

TWARIT: An extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences

(2012) Rachamalla Maheedhar Reddy et al.   GENE

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

(2012) David A W Soergel et al.   ISME Journal

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

The gut microbiota in IBD

(2012) Chaysavanh Manichanh et al.   Nature Reviews Gastroenterology & Hepatology

Rapid identification of high-confidence taxonomic assignments for metagenomic data

(2012) Norman J. MacDonald et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

(2012) Jiemeng Liu et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin

(2012) Vineet K. Sharma et al.   PLoS One

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

(2012) Kaustubh Raosaheb Patil et al.   PLoS One

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

(2012) Colin F. Davenport et al.   PLoS One

A Statistical Framework for Accurate Taxonomic Assignment of Metagenomic Sequencing Reads

(2012) Hongmei Jiang et al.   PLoS One

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

METAGENOMIC TAXONOMIC CLASSIFICATION USING EXTREME LEARNING MACHINES

(2012) ZEEHASHAM RASHEED et al.   Journal of Bioinformatics and Computational Biology

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

OTUbase: an R infrastructure package for operational taxonomic unit data

(2011) D. Beck et al.   BIOINFORMATICS

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

(2011) Xiaolin Hao et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

(2011) David J Russell et al.   BMC BIOINFORMATICS

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

(2011) Surendra Kumar et al.   BMC BIOINFORMATICS

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

(2011) Mohammadreza Ghodsi et al.   BMC BIOINFORMATICS

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences

(2011) Monzoorul Mohammed et al.   BMC GENOMICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Five commercial DNA extraction systems tested and compared on a stool sample collection

(2011) Søren Persson et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

(2011) Yunpeng Cai et al.   NUCLEIC ACIDS RESEARCH

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering

(2011) David R. Kelley et al.   NUCLEIC ACIDS RESEARCH

ClaMS: A Classifier for Metagenomic Sequences

(2011) Amrita Pati et al.   Standards in Genomic Sciences

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

JAGUC — A SOFTWARE PACKAGE FOR ENVIRONMENTAL DIVERSITY ANALYSES

(2011) MARKUS E. NEBEL et al.   Journal of Bioinformatics and Computational Biology

Treephyler: fast taxonomic profiling of metagenomes

(2010) F. Schreiber et al.   BIOINFORMATICS

SPHINX—an algorithm for taxonomic binning of metagenomic sequences

(2010) Monzoorul Haque Mohammed et al.   BIOINFORMATICS

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

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

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

(2010) Johannes Goll et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences

(2010) Tarini Ghosh et al.   BMC BIOINFORMATICS

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

(2010) Manuel Stark et al.   BMC GENOMICS

Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

(2010) Marc Weber et al.   ISME Journal

PANGEA: pipeline for analysis of next generation amplicons

(2010) Adriana Giongo et al.   ISME Journal

Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives

(2010) A. Salonen et al.   MICROBIOLOGY-SGM

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens

(2010) Merlin W Ariefdjohan et al.   Nutrition Journal

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

(2009) Erik Kristiansson et al.   BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Analysis and comparison of very large metagenomes with fast clustering and functional annotation

(2009) Weizhong Li   BMC BIOINFORMATICS

Metagenomic Pyrosequencing and Microbial Identification

(2009) J. F. Petrosino et al.   CLINICAL CHEMISTRY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Orphelia: predicting genes in metagenomic sequencing reads

(2009) Katharina J. Hoff et al.   NUCLEIC ACIDS RESEARCH

AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS

(2009) YUZHEN YE et al.   Journal of Bioinformatics and Computational Biology

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Binning sequences using very sparse labels within a metagenome

(2008) Chon-Kit Chan et al.   BMC BIOINFORMATICS

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

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

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY