GraphBin: refined binning of metagenomic contigs using assembly graphs

SolidBin: improving metagenome binning with semi-supervised normalized cut

(2019) Ziye Wang et al.   BIOINFORMATICS

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Simulating Illumina Metagenomic Data with InSilicoSeq

(2018) Hadrien Gourlé et al.   BIOINFORMATICS

Metagenomic binning through low-density hashing

(2018) Yunan Luo et al.   BIOINFORMATICS

Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities

(2018) Tyler P. Barnum et al.   ISME Journal

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation

(2017) Cedric C. Laczny et al.   NUCLEIC ACIDS RESEARCH

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

(2017) John Vollmers et al.   PLoS One

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

(2017) Karel Sedlar et al.   Computational and Structural Biotechnology Journal

MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures

(2016) Samuele Girotto et al.   BIOINFORMATICS

Assembly of long error-prone reads using de Bruijn graphs

(2016) Yu Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Large-scale machine learning for metagenomics sequence classification

(2015) Kévin Vervier 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

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

(2015) Rachid Ounit et al.   BMC GENOMICS

Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads

(2015) Vimac Nolla-Ardèvol et al.   BMC MICROBIOLOGY

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

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

(2015) Dongwan D. Kang et al.   PeerJ

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

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

(2014) Yu-Wei Wu et al.   Microbiome

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

MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species

(2012) Yi Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

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

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

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

(2011) Isaam Saeed et al.   NUCLEIC ACIDS RESEARCH

Clustering metagenomic sequences with interpolated Markov models

(2010) David R Kelley et al.   BMC BIOINFORMATICS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY