xGDBvm

A cloud-enabled genome annotation platform

xGDBvm is a web-based platform for annotating and visualizing eukaryotic genomes. xGDBvm is available through the iPlant/CyVerse Atmosphere platform, and leverages additional NSF XSEDE cyberinfrastructure resources such as the iPlant Data Store and the Agave API to high-performance computing provided by the Texas Advanced Computing Center.

Users can deploy an xGDBvm virtual machine (VM) on-demand, upload and validate their data, and configure their genome database. xGDBvm's processing pipeline can then compute spliced alignments of transcripts and proteins to the genome and annotate genes. Alternatively, users can supply pre-computed alignments and/or gene models. When the initial processing is complete, xGDBvm provides a fully-featured analysis platform including a genome browser, a web-based community annotation portal, a BLAST server, keyword search features, and more.

What can I do with xGDBvm?

• If you're interested in using xGDBvm in your research, start with the following.
  • xGDBvm video tutorials
  • xGDBvm case studies
• If you're already using xGDBvm and you have questions or technical issues, please open a thread on the xGDBvm issue tracker.
• If you're curious about xGDBvm's technical inner workings or want to contribute to the software development, check out the GitHub repository.

Reference

Duvick J, Standage DS, Merchant N, Brendel VP (2016) xGDBvm: A Web GUI-driven workflow for annotating eukaryotic genomes in the cloud. The Plant Cell, 28, 840-854 [online article].