AgAnimalGenomes.org provides tools based on JBrowse and Apollo that allow livestock genomics researchers to browse and manually annotate livestock genome assemblies. While a login is required to edit and create new annotations with Apollo, anyone can view the genomes and all data tracks (e.g. genes, gene expression, functional annotation, QTL, SNP, repeats) in JBrowse without logging in, via the links in JBrowse/Apollo pulldown menu.
The Apollo annotation tool is a plugin for JBrowse that allows registered users to manually edit transcripts or add new genes or transcripts. If you would like to register to submit gene corrections or new annotations, access the registration page in the Apollo Registration pulldown menu. After you submit the registration form, we will activate your account and send you an email. Once your account is activated, you can use the JBrowse/Apollo pulldown menu to select a genome, then login using a link in the upper right corner of the JBrowse view.
Those who wish to view and export existing user annotations can login to Apollo from any of the browsers in the JBrowse/Apollo pulldown menu with the username aganimal_guest and password guest. This will not allow editing genes or annotating new genes.
Demo browsers are available for practice annotation. See About Apollo Demos under the Tutorial and Demo pulldown menu.
If you use any of these browsers, please cite the genome as data you used, as well as the following article:
Triant DA, Walsh AT, Hartley GA, Petry B, Stegemiller MR, Nelson BM, McKendrick MM, Fuller EP, Cockett NE, Koltes JE, McKay SD, Green JA, Murdoch BM, Hagen DE, Elsik CG. AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome (2023). https://doi.org/10.1007/s00335-023-10008-1.
Please contact us if you have questions or suggestions.