Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

Diurnal Changes in Active Carbon and Nitrogen Pathways Along the Temperature Gradient in Porcelana Hot Spring Microbial Mat

(2018) María E. Alcamán-Arias et al.   Frontiers in Microbiology

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

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms

(2016) Javier Tamames et al.   Frontiers in Microbiology

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

(2015) Dinghua Li et al.   BIOINFORMATICS

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Attenuation of species abundance distributions by sampling

(2015) H. Shimadzu et al.   Royal Society Open Science

TIPP: taxonomic identification and phylogenetic profiling

(2014) Nam-phuong Nguyen et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads

(2014) Rogan Carr et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Taxonomy becoming a driving force in genome sequencing projects

(2013) Javier Tamames et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metagenomic Analysis of Stress Genes in Microbial Mat Communities from Antarctica and the High Arctic

(2011) Thibault Varin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Individual genome assembly from complex community short-read metagenomic datasets

(2011) Chengwei Luo et al.   ISME Journal

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

(2011) Rachel Mackelprang et al.   NATURE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Metagenomic profiling of Arctic microbial mat communities as nutrient scavenging and recycling systems

(2010) Thibault Varin et al.   LIMNOLOGY AND OCEANOGRAPHY

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics reveals our incomplete knowledge of global diversity

(2008) M. Pignatelli et al.   BIOINFORMATICS