MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

NanoSim: nanopore sequence read simulator based on statistical characterization

(2017) Chen Yang et al.   GigaScience

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

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Next generation sequencing data of a defined microbial mock community

(2016) Esther Singer et al.   Scientific Data

Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics

(2015) Matthias Willmann et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The inner workings of the hydrazine synthase multiprotein complex

(2015) Andreas Dietl et al.   NATURE

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

(2015) Dongwan D. Kang et al.   PeerJ

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Frameshift alignment: statistics and post-genomic applications

(2014) Sergey L. Sheetlin et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Evolution of Pan-Genomes of Escherichia coli, Shigella spp., and Salmonella enterica

(2013) E. N. Gordienko et al.   JOURNAL OF BACTERIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic approaches to studying the human microbiota

(2012) George M. Weinstock   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE