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

Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches

(2016) Vera Tai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

(2016) J. A. Frank et al.   Scientific Reports

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

(2016) Ivan Gregor et al.   PeerJ

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

(2016) Anna Heintz-Buschart et al.   Nature Microbiology

Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens

(2016) Stéphane Deschamps et al.   Scientific Reports

Elviz – exploration of metagenome assemblies with an interactive visualization tool

(2015) Michael Cantor et al.   BMC BIOINFORMATICS

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

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

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

(2015) Phelim Bradley et al.   Nature Communications

Scaffolding of a bacterial genome using MinION nanopore sequencing

(2015) E. Karlsson et al.   Scientific Reports

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

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

(2015) Andy Kilianski et al.   GigaScience

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

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

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

(2014) Emilie E. L. Muller et al.   Nature Communications

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

(2013) Migun Shakya et al.   ENVIRONMENTAL MICROBIOLOGY

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Wide Variation in Antibiotic Resistance Proteins Identified by Functional Metagenomic Screening of a Soil DNA Library

(2012) Kelly M. McGarvey et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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 and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin

(2012) Vineet K. Sharma et al.   PLoS One

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

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

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick 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