The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology

(2017) Benjamin J. Tully et al.   PeerJ

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

(2017) Elaina D. Graham et al.   PeerJ

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

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

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

(2016) Kiley W Seitz et al.   ISME Journal

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

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

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

The global ocean microbiome

(2015) M. A. Moran   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

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

(2015) A. Murat Eren et al.   PeerJ

Open science resources for the discovery and analysis of Tara Oceans data

(2015) Stéphane Pesant et al.   Scientific Data

Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers

(2014) M. A. Saito et al.   SCIENCE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Expression patterns reveal niche diversification in a marine microbial assemblage

(2012) Scott M Gifford et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE