G-OnRamp

G-OnRamp facilitates collaborative eukaryotic genome annotation by integrating evidence tracks from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders for visualization in UCSC Assembly Hubs and JBrowse/Apollo genome browsers.

Key Features:

• End-to-end annotation: Supports the full genome annotation workflow from input data processing to annotation output.
• Evidence track integration: Integrates sequence alignments, ab initio gene predictors, RNA-Seq-derived evidence, and repeat finder results into composite evidence tracks.
• Genome browser visualization: Generates UCSC Assembly Hubs and configures JBrowse/Apollo genome browsers to display evidence tracks.
• Collaborative annotation: Supports collaborative curation of gene models via Apollo, allowing multiple users to contribute to shared annotations.

Scientific Applications:

• Collaborative genome annotation projects: Supports eukaryotic genome annotation projects that require integrating multiple evidence types across contributors.
• Gene structure prediction: Facilitates prediction and refinement of gene models by combining sequence alignments, ab initio predictions, and RNA-Seq evidence.
• Educational genomics: Enables hands-on annotation exercises for teaching genomics and bioinformatics using real datasets.

Methodology:

Generates evidence tracks from sequence alignments, ab initio gene prediction, RNA-Seq data analysis, and repeat detection, and visualizes them using JBrowse/Apollo and UCSC Assembly Hubs.