Two-day Virtual Workshop

25-26 April 2022

About the workshop

A two-day course that will cover the processes of phage genome assembly, annotation and introduction to comparative phage genome analysis.

Solutions to common phage genome assembly problems will be presented, through worked examples.

Attendees can bring their own phage genomes or raw reads to assemble. Please indicate in the application form if you plan to do this. 

When: 25-26 April 2022, time 11am – 5pm (BST)

Where: Online, on Zoom. Participation links will be sent to the selected participants closer to the event.

Instructor: Dr Andy Millard, University of Leicester

Selected participants have already been contacted and will be updated with the full programme before the workshop.

Prerequisites

Basic understanding of Linux commands (able to create files and directories).

Preliminary Programme

The final programme and schedule will be uploaded ASAP on this webpage.

Day 1 – Topics

Quality control of read data. Subsampling of reads. Assembly of phage genome. Preliminary identification of closest relatives. Identification of genomic termini re-ordering of genome.  

Day 2 – Topics

Error correction of genome assembly. First pass automated annotation. Checking Annotations. Preparation of files for submission to ENA. Comparative genomics. Visualization of genomes

Suggested pre-reading

https://www.liebertpub.com/doi/10.1089/phage.2021.0013
https://www.liebertpub.com/doi/10.1089/phage.2021.0015
https://www.liebertpub.com/doi/10.1089/phage.2021.0008
https://www.mdpi.com/1999-4915/14/2/342

Websites
www.phagecompass.dk
https://github.com/gamcil/clinker