BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

(2016) Benjamin J. Tully et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge

(2016) Yang Young Lu et al.   BIOINFORMATICS

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

(2016) Julie L. Meyer 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

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

(2015) Robert M. Bowers et al.   BMC GENOMICS

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

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

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center

(2015) Karthik Anantharaman et al.   ISME Journal

Subspace clustering using affinity propagation

(2015) Guojun Gan et al.   PATTERN RECOGNITION

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

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

(2015) Dongwan D. Kang et al.   PeerJ

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

Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data

(2014) Benjamin J Tully et al.   Microbiome

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

(2014) Brandon Brooks et al.   Microbiome

Clustering in Vehicular Ad Hoc Networks using Affinity Propagation

(2013) B. Hassanabadi et al.   Ad Hoc Networks

IMG 4 version of the integrated microbial genomes comparative analysis system

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Analysis of intra-genomic GC content homogeneity within prokaryotes

(2010) Jon Bohlin et al.   BMC GENOMICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Barcodes for genomes and applications

(2008) Fengfeng Zhou et al.   BMC BIOINFORMATICS