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

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

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

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

(2014) Yu-Wei Wu et al.   Microbiome

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

(2013) Scott C. Clark et al.   BIOINFORMATICS

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Dietary intervention impact on gut microbial gene richness

(2013) Aurélie Cotillard et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Classification of metagenomic sequences: methods and challenges

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

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples

(2011) Yu-Wei Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

(2011) Isaam Saeed et al.   NUCLEIC ACIDS RESEARCH

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers

(2010) Bin Yang et al.   BMC BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Phylogenetic Signals in DNA Composition: Limitations and Prospects

(2009) J. Mrazek   MOLECULAR BIOLOGY AND EVOLUTION

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY