GenomeHubs

GenomeHubs provides a containerized platform to set up and host custom Ensembl genome browsers for importing, mirroring, annotating, and exporting genomic datasets (FASTA, GFF, EMBL) for non-model organisms and comparative genomics, including submission to INSDC.

Key Features:

• Containerized Environment: Provides containerized deployment of Ensembl databases and web servers.
• Custom Ensembl Browsers: Mirrors existing Ensembl content or imports new data into the Ensembl database schema to create tailored genome browsers.
• Data Import and Mirroring: Supports import and mirroring of FASTA and GFF files and integration of datasets such as the Glanville fritillary (Melitaea cinxia) and the winter moth (Operophtera brumata).
• Analysis Containers: Includes analysis containers that perform standard analyses and add functional annotations to imported genomes.
• Data Export Options: Exports flat files including EMBL format to support assembly and annotation submission to INSDC.

Scientific Applications:

• Non-model organism genome hosting: Hosts custom Ensembl browsers for genome projects focused on non-model organisms.
• Comparative genomics: Enables cross-species analyses through integrated Ensembl schema and imported annotations.
• Assembly and annotation submission: Produces EMBL and other flat-file exports for submission of assemblies and annotations to INSDC.
• Integration of community datasets: Consolidates genomic datasets from multiple projects into a consistent Ensembl-based database.

Methodology:

GenomeHubs leverages the Ensembl platform, employs containerization to deploy Ensembl databases and web servers, imports and mirrors FASTA and GFF datasets into the Ensembl schema, uses analysis containers to run standard analyses and functional annotation, and exports flat files including EMBL for INSDC submission.