Workshop on viral genomics and taxonomy

Turner, Dann; Adriaenssens, Evelien M.; Kropinski, Andrew M.

Abstract

How many of us have isolated and sequenced a phage, gotten reads back from the sequencing facility and thought "What now?" How can I assemble the data, and should I use an automated pipeline (DFAST, RASTtk, PHANOTATE) to annotate the genome, or shall I do what my scientific ancestors in the laboratory did before me and manually scan for ORFs, Shine-Dalgarno sequences, promoters and terminators? What if there is no reference phage closely related to mine? What if there is? What is a phage species and what about all those new families?

In this workshop, we will try to guide you through the whole process, from deciding on the sequencing technology, to assembly, annotation and classification. For the most part, we will use Internet resources and freely available software that can be run on a laptop computer. We9ll teach you how to hunt for missing coding sequences and false start codons, show best practices in functional annotation and drill down the mantra "if you cannot convince your grandmother (Avó) of a protein's function, call it hypothetical protein".

In the second part of the workshop, we'll introduce the participants into the wonderful – if somewhat baffling – world of official virus taxonomy. We'll highlight some of the new tools that are available and guide you through the decision-making process.

At the end of this workshop, you will have all the knowledge and tools to go from a sequence file to a finished annotated phage genome that can be submitted to an INSDC database and can be officialised through a Taxonomy Proposal to ICTV (the International Committee on Taxonomy of Viruses).

The workshop coordinators are Chair, Vice Chair and former Chair of ICTV's Bacterial Viruses Sub-committee and members of NCBI's Viral Advisory Committee. In these capacities they are committed to assure that phage genomes submitted to NCBI are complete, accurate, properly annotated, and accurately classified.

Citation

Turner, D., Adriaenssens, E. M., & Kropinski, A. M. (2022, June). Workshop on viral genomics and taxonomy. Presented at Viruses of Microbes 2022, Guimaraes, Portugal

• Presentation Conference Type: Other
• Conference Name: Viruses of Microbes 2022
• Conference Location: Guimaraes, Portugal
• Start Date: Jun 22, 2022
• End Date: Jun 22, 2023
• Deposit Date: Jun 12, 2023
• Publicly Available Date: Jun 14, 2023
• Keywords: phage annotation, phage genomics, phage classification
• Public URL: https://uwe-repository.worktribe.com/output/10860135
• Related Public URLs: https://skyros-congressos.pt/vom2022/