GenomeHubs brings together a number of external tools and tools developed within the Blaxter Lab previously at the University of Edinburgh and now at the Wellcome Sanger Institute.

Ensembl genome browser

Ensembl is a fully-featured genome browser produced by EMBL-EBI. The main public instance of this browser hosts a curated collection of vertebrate genomes while related EMBL-EBI hosted sites are available for Metazoa, Plants, Bacteria, Protists and Fungi. Each GenomeHubs site uses an Ensembl browser to display assemblies and runs code using the associated API to validate and standardise data during the import process.

SequenceServer BLAST server

SequenceServer is a user-friendly and flexible interface to run NCBI BLAST searches across locally installed databases produced by Yannick Wurm’s lab. Scaffold, gene and protein sequences for each assembly in a GenomeHub are added to a SequenceServer instance as searchable BLAST databases. The SequenceServer instance acts as an entry point to a GenomeHub for sequence-based queries while links to and from the Ensembl instance allow exploration of homologous regions across all available assemblies.

h5ai downloads server

h5ai is a lightweight directory indexer written by Lars Jung. Sequence and analysis files are added to a standard directory hierarchy during the GenomeHubs assembly import process and the root directory is then hosted in an h5ai instance to provide a simple, browsable interface to bulk downloads.

BlobToolKit interactive assembly visualisation

BlobToolKit is a toolkit for interactive exploration and filtering of draft and published assemblies written by Richard Challis in the Blaxter Lab. We plan to integrate this more closely with GenomeHubs over the coming months.

OrthoFinder inference of orthology

OrthoFinder by David Emms and Steve Kelly infers orthology and provides a flexible framework for producing gene and species trees from these inferred orthogroups. In a departure from the Ensembl methodology, GenomeHubs sites use and OrthoFinder-based analysis of protein sequences to provide orthology information and gene trees. All information is imported into a standard Ensembl Compara database so GenomeHubs can use the full set of Ensembl comparative views.

KinFin analysis of clustered protein sequences

KinFin is a tool for analysis of clustered protein sequences written by Dom Laetsch in the Blaxter Lab. We plan to integrate this more closely with GenomeHubs over the coming months.