Teachers
Martha Clokie
Professor
Heera Rajandas
Associate Professor
June 1 - June 7
The Computational Phage Genomics Programme 2024 offers hands-on experience analysing phage genome sequencing data,
from raw NGS reads to a fully assembled and annotated phage genome.
The course includes lectures and computer exercises
This is a course with physical attendance only, at the University of Copenhagen, Denmark
The majority of exercises will be performed within a UNIX terminal. This optional module aims to provide you with a fundamental grasp of UNIX and terminal operations.
This module includes introductions, lectures on phage biology and sequence analysis, followed by practical exercises in data retrieval, quality control, and de-novo sequence assembly.
In this module attendees will delve into phage therapy and genomics through lectures, followed by practical exercises covering open reading frame predictions, protein function prediction, genome reordering, and automated workflows, including hands-on work with your own data.
This module focuses on tackling scenarios with no sequence similarity and comparing phage genomes within the CSR framework. Attendees will engage practical exercises, including prediction of protein structures, machine learning-based function predictions, and hands-on exploration of their own phage proteomes.
This module begins with a general introduction to phage taxonomy and a historical perspective on phage therapy. Attendees will engage in practical exercises covering phylogeny with marker genes, inferring taxonomy through gene sharing networks, complete genome phylogeny, and visualizing phage genome space with PhageClouds.
This module is dedicated to preparing ENA/NCBI submissions. It begins with an introduction to ENA and NCBI. Participants will learn how to prepare phage genomes for submission to ENA/NCBI.
Both days: 10.00 - 16.00 (Attendance at both sessions are voluntary)
Software installation day 1:
We'll be utilizing specialized software throughout the course, so it's advisable to have it installed prior to Monday's course commencement. Should you encounter any difficulties during installation, we are here to assist you.
UNIX day 2:
The majority of exercises will be performed within a UNIX terminal. This optional session aims to provide you with a fundamental grasp of UNIX and terminal operations.
09:00 - 09.30 Welcome and general introduction
09.30 - 10.00 Round of introduction (All teachers + participants)
Lectures
10.00 - 10.45 A general introduction to phage biology
10.45 - 11.00 Questions and discussion
11.00 - 11.15 Coffee break
11.15 - 12.00 A general introduction to sequence analysis
12.00 - 12.15 Questions and discussion
12.15 - 13.15 Lunch
Sequence analysis (short talks + computer exercises)
13.15 - 13.45 Retrievement of rainforest phages sequence data - Where is the data from?
13:45 - 14:45 Quality control and cleaning of sequence data
14:45 - 15.00 Coffee Break
15:00 - 15:30 QC on your own sequence data (All Participants)
15:30 - 16.30 De-novo sequence assembly
16:30 - 17:00 De-novo assembly on your own sequence data
17.00 - 17.30 Questions and discussion
Lectures
09:00 - 09:45 A general introduction to phage therapy
09:45 - 10:00 Questions and discussion
10:00 - 10:45 A general introduction to phage genomics
10:45 - 11:00 Questions and discussion
11.00 - 11.15 Coffee break
11:15 - 12:15 Day 3 Recap
12.15 - 13.15 Lunch
Phage genome annotation (short talks + computer exercises)
13:15 - 14:00 Predictions of open reading frames
14:00 - 14:45 Prediction of protein function by homology
14:45 - 15.00 Coffee Break
15:00 - 15:45 Reordering the phage genome
15:45 - 16:15 Automated workflows
16:15 - 17:00 Automated workflow on your own data
17.00 - 17.30 Questions and discussion
Lectures
09:00 - 09:45 When there is no sequence similarity
09:45 - 10:00 Questions and discussion
10:00 - 10:45 Comparing phage genomes in the CSR framework
10:45 - 11:00 Questions and discussion
11.00 - 11.15 Coffee break
11:15 - 12:15 Day 4 Recap
12.15 - 13.15 Lunch
13:15 - 14:00 Prediction of phage protein structures,
14:00 - 14:45 Machine learning-based function predictions
14:45 - 15.00 Coffee Break
15:00 - 17:00 Exploring your own phage proteome (All Participants)
17.00 - 17.30 Questions and discussion
09:00 - 09:45 A general introduction to phage taxonomy
09:45 - 10:00 Questions and discussion
10:00 - 10:45 Phage therapy - then and now
10:45 - 11:00 Questions and discussion
11.00 - 11.15 Coffee break
11:15 - 12:15 Day 5 Recap
12.15 - 13.15 Lunch
13:15 - 14:00 Phylogeny with marker genes
14:00 - 14:45 Inferring taxonomy by gene sharing networks
14:45 - 15.00 Coffee Break
15:00 - 16:15 Complete genome phylogeny
16:15 - 17:00 Visualising phage genome space - PhageClouds
09:00 - 09:45 A general introduction to ENA and NCBI
09:45 - 10:00 Questions and discussion
10:00 - 10:45 Day 6 Recap
11.00 - 11.15 Coffee break
11:15 - 12:15 Preparing phage genomes for ENA/NCBI submission
12.15 - 13.15 Lunch
13:15 - 14:00 Preparing phage genomes for ENA/NCBI submission
14:00 - 14:30 Final reflections and how to continue
14:30 Departure
- Understanding of basic phage biology
- Basic understanding of genome sequencing
- Participants should bring their own laptops. Software requirements will be communicated before the course and help with software installation will be done online Friday, October 27th.
- A basic understanding of working with the command line on UNIX-based systems like Linux, Mac, or Windows Subsystem for Linux (WSL). If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals pre-workshop module Saturday, October 28th.
Throughout the course, participants will retrieve newly sequenced phage genomes, collected in the Malaysian rainforests (https://www.combio-aimst.my). Participants are encouraged to bring their own phage genome sequencing data (Illumina, PE).
Martha Clokie
Professor
Heera Rajandas
Associate Professor
Bent Petersen
Senior Researcher, PhD
Thomas Sicheritz-Pontén
Professor
Andrew Millard
Associate Professor