iMicrobe: Tools and data-driven discovery platform for the microbiome sciences

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

(2018) Joel A Boyd et al.   NUCLEIC ACIDS RESEARCH

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Libra: scalable k-mer based tool for massive all-vs-all metagenome comparisons

(2018) Illyoung Choi et al.   GigaScience

Putative archaeal viruses from the mesopelagic ocean

(2017) Dean R. Vik et al.   PeerJ

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

Environmental drivers of a microbial genomic transition zone in the ocean’s interior

(2017) Daniel R. Mende et al.   Nature Microbiology

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Protocols.io: Virtual Communities for Protocol Development and Discussion

(2016) Leonid Teytelman et al.   PLOS BIOLOGY

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

(2016) Nirav Merchant et al.   PLOS BIOLOGY

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

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

(2015) Dinghua Li et al.   BIOINFORMATICS

The MG-RAST metagenomics database and portal in 2015

(2015) Andreas Wilke et al.   NUCLEIC ACIDS RESEARCH

UProC: tools for ultra-fast protein domain classification

(2014) Peter Meinicke   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

IMG 4 version of the integrated microbial genomes comparative analysis system

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

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH