Community-led, integrated, reproducible multi-omics with anvi’o

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

(2020) Vahid Jalili et al.   NUCLEIC ACIDS RESEARCH

The Wolbachia mobilome in Culex pipiens includes a putative plasmid

(2019) Julie Reveillaud et al.   Nature Communications

Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade

(2019) Tom O Delmont et al.   eLife

Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus)

(2019) Carl J. Yeoman et al.   PeerJ

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

U-Index, a dataset and an impact metric for informatics tools and databases

(2018) Alison Callahan et al.   Scientific Data

The past, present and future of microbiome analyses

(2016) Richard Allen White et al.   Nature Protocols

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

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

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

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

(2015) A. Murat Eren et al.   PeerJ

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Wolbachia: master manipulators of invertebrate biology

(2008) John H. Werren et al.   NATURE REVIEWS MICROBIOLOGY