GenomeHubs

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. Database, 2017:bax039 doi:10.1093/database/bax039

Current GenomeHubs

Coming soon...

  • MolluscDB

Connected GenomeHubs

Linking GenomeHubs

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.

Lepbase

Our flagship site provides a home for Lepidopteran genome assemblies.

visit lepbase.org to find out more or go straight to the LepBase Ensembl

Caenorhabditis Genomes Project

A project to sequence all the species in the genus Caenorhabditis.

visit caenorhabditis.org to find out more or go straight to the CGP Ensembl

Documentation

Documentation for GenomeHubs setup and configuration is available at genomehubs.gitbooks.io.

A more general description is available in our paper in Database:
Challis RJ, Kumar S, Stevens L & Blaxter M (2017) GenomeHubs: Simple containerised setup of a custom Ensembl database and web server for any species. Database, 2017:bax039 doi:10.1093/database/bax039

All GenomeHubs code is open-source and can be found in our GitHub repositories at github.com/genomehubs.

For a detailed description of the EasyImport scripts used to import new assemblies from FASTA and GFF, see our documentation on readme.io.

Blog