GenomeHubs have been developed as part of the LepBase project to provide a simple and scalable way to deploy an Ensembl genome browser and associated tools for clades or communities of non-model organisms.
Challis RJ, Kumar S, Stevens L & Blaxter M (2017) GenomeHubs: Simple containerised setup of a custom Ensembl database and web server for any species. PeerJ Preprints, 5:e2401v2 doi:10.7287/peerj.preprints.2401v2
- lepbase.org - the lepidopteran genome database
- ensembl.caenorhabditis.org - an Ensembl for the Caenorhabditis Genomes Project which aims to sequence all species in the genus Caenorhabditis
- ensembl.tardigrades.org - an Ensembl to support collaboration on tardigrade genome sequencing
- ensembl.ngenomes.org - a selection of recent genome assemblies from the Blaxter Lab
- ensembl.mealybug.org - a model system for host-symbiont interaction
- MolluscDB - combining transcriptome and genome sequence data for over 300 species of Mollusc
As more taxa are included in Ensembl genome browsers through GenomeHubs, individual hubs will increasingly be linked by shared taxa, whether included as focal species, reference assemblies or outgroups. By including shared taxa in comparative analyses (gene trees and whole genome alignments) run and imported into the Ensembl compara database format using GenomeHubs containers, a network of GenomeHubs will provide a substantial resource for comparative analyses. Having the data in a standardised format and accessible through the Ensembl API will open up opportunities to discover phylogenetically independent contrasts and to test hypotheses developed in a single clade by running the same API scripts on additional clades for which suitable data are available.