BCC2020

➞ Abstract

Jolene Ramsey 1,2, Cory Maughmer 1,2, Anthony Criscione 1,2, Mei Liu 1,2, Ry Young 1,2, Jason J. Gill 1,3

1. Center for Phage Technology, Texas A&M University, College Station, Texas, USA
2. Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
3. Department of Animal Science, Texas A&M University, College Station, Texas, USA

The presenter(s) will be available for live Q&A at the end of this session (BCC West).
In the modern genomic era, scientists without extensive bioinformatic training need to apply advanced computational analyses to genome annotation. At the Center for Phage Technology (CPT), we use two open source, web-based platforms: Galaxy, for reproducible computational analyses, and Apollo, a collaborative genome annotation editor, to facilitate annotation of phage genomes. The development and expansion of the Galaxy-Apollo bridge has been discussed at prior Galaxy Community Conferences, and the critical contributions by many former and current community members are gratefully acknowledged. In this presentation, we will describe how scientists and students have been trained to use semi-automated workflows in Galaxy and Apollo for collaborative annotation of genomes, including feature calling, contextualized functional prediction, and comparative genomics.
Unlike the genomes of most cellular life forms, phage genomes are usually a single contiguous molecule <200,000 bases in length. Their size allows high standards for complete, evidence-based annotations, and is amenable to genomics education settings. The CPT Galaxy and Apollo system is used for original biological research and development of new bioinformatic tools to analyze many individual phage genomes, as well as clusters of related phages. Our robust suite of phage-oriented tools includes open source applications such as PhageTerm, as well as unique programs for finding Shine-Dalgarno sequences, a collection of tools used for confident identification of lysis genes, and identification of interrupted genes that contain frameshifts or introns. The step-wise process moves all aspects of control and choice into the user’s court. In comparison to widely used automated and fast command-line annotation methods, our integrated and flexible approach benefits from trained human intervention to result in high-quality final annotations.
The CPT has educated a steady stream of scientists, as well as both undergraduate and graduate students, informally and through formal university course offerings on using this Galaxy-Apollo infrastructure to annotate phage genomes. The resulting data, continuously collated on our BioProject page (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA222858), is deposited in public sequence repositories and published regularly. By creating a free user account, local or international teams can begin their own analyses. Accompanying user training material in the Galaxy Training Network format is hosted at https://cpt.tamu.edu/training-material/.
Project Website: https://cpt.tamu.edu/galaxy-pub