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

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

(2015) Rachid Ounit et al.   BMC GENOMICS

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Consistency of metagenomic assignment programs in simulated and real data

(2014) Koldo Garcia-Etxebarria et al.   BMC BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

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

A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA

(2013) D. H. Huson et al.   BIOINFORMATICS

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

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

(2013) Christina Ander et al.   BMC BIOINFORMATICS

AmphoraNet: The webserver implementation of the AMPHORA2 metagenomic workflow suite

(2013) Csaba Kerepesi et al.   GENE

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Real Time Metagenomics: Using k-mers to annotate metagenomes

(2012) Robert A. Edwards et al.   BIOINFORMATICS

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Analysis of composition-based metagenomic classification

(2012) Susan Higashi et al.   BMC GENOMICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Rachamalla Maheedhar Reddy et al.   GENE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Rapid identification of high-confidence taxonomic assignments for metagenomic data

(2012) Norman J. MacDonald 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

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

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem

(2011) Seungdae Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

(2011) Beifang Niu et al.   BIOINFORMATICS

Classifying short genomic fragments from novel lineages using composition and homology

(2011) Donovan H Parks et al.   BMC BIOINFORMATICS

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

(2011) Suparna Mitra 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

Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems

(2011) Renee J. Smith et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River

(2011) Rohit Ghai et al.   PLoS One

ClaMS: A Classifier for Metagenomic Sequences

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

SPHINX—an algorithm for taxonomic binning of metagenomic sequences

(2010) Monzoorul Haque Mohammed et al.   BIOINFORMATICS

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

(2010) G. L. Rosen et al.   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

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

(2010) S. Sun et al.   NUCLEIC ACIDS RESEARCH

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

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

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

Visual and statistical comparison of metagenomes

(2009) Suparna Mitra et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Methods for comparative metagenomics

(2009) Daniel H Huson et al.   BMC BIOINFORMATICS

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

(2009) Wolfgang Gerlach et al.   BMC BIOINFORMATICS

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

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

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY