AgAnimalGenomes.org provides tools based on JBrowse and Apollo that allow livestock genomics researchers to browse and manually annotate livestock genome assemblies.
The Apollo annotation tool is a plugin for JBrowse that allows registered users to manually edit transcripts or add new genes or transcripts. The genome browsers provided by AgAnimalgenomes.org also include a plugin called Apollo-LSAA ("Locus Specific Alternate Assembly"), which allows registered users to submit information about genome assembly errors or structural variations. While only registered users can submit data or access pre-release submitted genome annotations, all users can view the genomes with JBrowse, via the links in the navigation bar.
If you would like to register to submit gene or assembly corrections, use the Apollo Registration pull down menu to select an organism. Once you are registered, you can use the JBrowse/Apollo menu to select a genome, then login using a link in the upper right corner of the JBrowse view.
Note that Sheep Oar_v3.1 and Oar_v4.0 are not available for Apollo annotation because a new reference sheep genome will be available in the near future.