GenomeHubs

The GenomeHubs project provides tools for visualising and interpreting genomic datasets

GenomeHubs version 2 comprises a set of tools to parse, index, search, and display genomic metadata, and assembly features for all eukaryotic genome assemblies, and to help coordinate efforts across the Earth Biogenome Project Network at all stages from planning through sequencing and assembly to publication. GenomeHubs tools include Genomes on a Tree and BlobToolKit.

GenomeHubs

Version 2

Since version 2.0, GenomeHubs is search-oriented and positioned to scale to the challenges of mining data across the approximately 2 million described eukaryotic species.

The first output from the new search-oriented GenomeHubs is Genomes on a Tree (GoaT, Challis et al. 2023), available at goat.genomehubs.org. GoaT is freely available without logins or restrictions, and is being widely used by the academic community and especially by the Earth BioGenome Project to plan and coordinate efforts to sequence all described eukaryotic species.

Version 1

The first version of GenomeHubs (Challis et al. 2017) was designed to make it easy to set up and host a core set of bioinformatics tools to help research communities share and access genomic datasets for non-model organisms. This approach was originally developed during the BBSRC funded LepBase project as a solution to creating a genome browser and BLAST server for the Lepidopteran research community.

GenomeHubs v1 currently powers lepbase.org, molluscdb.org, and mealybug.org. It uses Docker containers to deploy tools to view and search genomic datasets and a typical site has:

an Ensembl Genome Browser
a SequenceServer BLAST server
an h5ai downloads server

BlobToolKit

Alongside indexing and search, powered by the core GenomeHubs code, BlobToolKit (Challis et al. 2020), available at blobtoolkit.genomehubs.org aids analysis and interpretation of contaminant and cobiont sequences in genome assembly data. The main instance of the BlobToolKit viewer allows exploration of most publicly available Eukaryotic genome assemblies. We are making the data generated through analysis of these assemblies availableand accessible through GoaT and an assembly feature-oriented GenomeHubs instance, BoaT, currently in development.