PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

KMC 2: fast and resource-frugal k-mer counting

(2015) Sebastian Deorowicz et al.   BIOINFORMATICS

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

(2015) Rachid Ounit et al.   BMC GENOMICS

KAnalyze: a fast versatile pipelined K-mer toolkit

(2014) Peter Audano et al.   BIOINFORMATICS

Turtle: Identifying frequent k -mers with cache-efficient algorithms

(2014) Rajat Shuvro Roy et al.   BIOINFORMATICS

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

(2014) J. Dröge et al.   BIOINFORMATICS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

(2014) Genivaldo Gueiros Z. Silva et al.   PeerJ

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

The microbiome explored: recent insights and future challenges

(2013) Martin Blaser et al.   NATURE REVIEWS MICROBIOLOGY

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies

(2012) J. Droge et al.   BRIEFINGS IN BIOINFORMATICS

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Metagenomics with guts

(2012) Magdalena Zarowiecki   NATURE REVIEWS MICROBIOLOGY

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci

(2012) Phillip B. Pope et al.   PLoS One

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

(2012) Kaustubh Raosaheb Patil et al.   PLoS One

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell 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

Mixture models for analysis of the taxonomic composition of metagenomes

(2011) Peter Meinicke et al.   BIOINFORMATICS

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Integrative analysis of environmental sequences using MEGAN4

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

Genovo: De Novo Assembly for Metagenomes

(2011) Jonathan Laserson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies

(2011) P. B. Pope et al.   SCIENCE

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

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

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

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

(2010) Manuel Stark et al.   BMC GENOMICS

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

(2010) P. J. Turnbaugh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Cutting-plane training of structural SVMs

(2009) Thorsten Joachims et al.   MACHINE LEARNING

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

High-resolution metagenomics targets specific functional types in complex microbial communities

(2008) Marina G Kalyuzhnaya et al.   NATURE BIOTECHNOLOGY

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY