G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation
Fig 3
G-OnRamp is a Galaxy-based platform with analysis workflows that process a target genome assembly, transcripts and proteins from an informant genome, and RNA-Seq data from the target genome to create a genome browser for individual or collaborative annotation. Four sub-workflows (sequence similarity, ab initio gene predictions, RNA-Seq analysis, and repeats identification) run concurrently and generate the data for manual gene annotation. Data produced by the sub-workflows are used by the Hub Archive Creator (HAC) tool to create UCSC Assembly Hubs and by the JBrowse Archive Creator (JAC) to create JBrowse genome browsers. The Apollo interaction tools convert JBrowse genome browsers into an Apollo instance to facilitate collaborative annotations. Genome browsers produced by G-OnRamp can be transferred to the CyVerse Data Store via the CyVerse export tool for long-term storage and visualization. The “Tool Suites” panel (below) lists the primary tools in each sub-workflow and the tools provided by G-OnRamp to create and manage Apollo instances. See [20] and http://g-onramp.org for further details. RNA-Seq, RNA sequencing.