Computational Phage Genomics

Aim and content

This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee.

Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.

Learning objectives

Knowledge:
1. Understand the basic insights into phage therapy and put into perspective how bioinformatics can support the acceleration of the therapeutic use of phages
2. Understand the concept of phage taxonomy
3. Understand the context and implications of lack of sequence similarity

Skills:
1. Install and use programs in Unix for analysis of phage genomics data
2. Critically assess the quality of Next Generation Sequencing data
3. Be able to perform the most basic NGS analysis (de-novo assembly, gene finding, gene and genome annotation)
4. Preparing a phage genome for submission to ENA and NCBI

Participants
The target group is PhD students at Danish Universities and anybody interested from outside of Denmark as well:

Requirements:
– 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). If possible, participants are encouraged to bring their own phage genome sequencing data (Illumina, PE).

Relevance to graduate programmes
The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH:

All graduate programmes

Language
English

Form
Lectures and computer exercises

Course director
Bent Petersen: Senior Researcher, Globe institute, University of Copenhagen,
bent.petersen@sund.ku.dk

Teachers
Thomas Sicheritz-Pontén: Professor, Globe Institute, University of Copenhagen (DK)
Bent Petersen: Senior Researcher, Globe Institute, University of Copenhagen (DK)
Martha Clokie: Professor, University of Leicester (UK)
Andrew Millard: Associate Professor, University of Leicester (UK)
Heera Rajandas Associate Professor, AIMST University, (MY)
Gemma Atkinson Associate Professor, Lund University, (SE)

Dates
Pre-workshop Zoom sessions 1 and 2 June 2024
3 to 7 June 2024

Course location
The Globe Institute Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, University of Copenhagen Øster Farimagsgade 5, 1353 Copenhagen K, Denmark

Registration
Please register before 1 May 2024

Expected frequency
Twice per year

Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules.
Applications from other participants will be considered after the last day of enrolment.

Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

Disclaimer:
DDSA has explicit permission from Arcanic and the owners of the https://phdcourses.dk/ website to display the courses on ddsa.dk.