ckigenk/acorn-clinamr

Interactive training for functional analysis and interpretation of disease data using computational modelling tools

WCS ACORN - Bioinformatics for Antimicrobial Resistance - Virtual 21 May–6 June 2024

Interactive training for functional analysis and interpretation of disease data using computational modelling tools

Course Overview

Antimicrobial resistance (AMR) is critical to monitor as it threatens modern medical and public health systems. The Clinically Oriented antimicrobial Resistance Network (ACORN) project is developing an effective AMR surveillance system across nine African and Asian countries.

This course aims to train ACORN team members across nine centres with core bioinformatics skills which can be utilised to analyse and identify resistance from pathogen genome data.

This course is virtual and will run twice a week from 21 May until 6 June 2024

Course website

Course Content

This virtual bioinformatics course will offer a series of lectures and practical sessions including the following topics:

• Pathogen genome assembly
• Annotation of pathogen genomes
• Phylogenetics in clinical contexts

Learning Outcomes

At the end of this course, participants will be able to:

• Apply appropriate tools to analyse WGS data of bacterial genomes
• Identify sequencing data formats
• Use pathogen genomic analysis web-tools to process sequence data
• Execute the basic processes of genome assembly for pathogen species
• Identify and interrogate antibiotic resistance genes and mutations
• Implement data workflows and bioinformatic analysis of genomic sequence data, including risk and resistance prediction for bacterial epidemiology and pandemic response
• Conduct phylogenetic analysis in the context of outbreak and other epidemiological investigations
• Compare phylogenetic trees for different species and outbreak scenarios

Training Team

• Trinh Son Tung, Oxford University Clinical Research Unit (OUCRU)

• Patrick Musicha ,Sanger Institute, UK

• Julio Diaz,CPGR, UK

• Arun Decano,University of Oxford, UK

• Rito Mikhari,National Institute for Communicable Diseases, South Africa

• Collins Kigen,Kenya Medical Research Institute

• Buhle Ntozini,National Institute for Communicable Diseases, South Africa

• Jorge Batista da Rocha,Wellcome Connecting Science

• Trinh Son Tung, Oxford University Clinical Research Unit (OUCRU)

• Vaishnavi Vikas Gangadhar,Wellcome Connecting Science

• Isabela Malta,Wellcome Connecting Science

• Martin Aslett,Wellcome Connecting Science

• Alice Matimba,AWellcome Connecting Science

Detailed timetable

View Timetable here

Course Manual

Pre-Course Module Introduction to Linux for Biologists (ACORN)

Week 1
21 May Tuesday: Bash, File formats
GoogleCollabNotebook
Slides
Lecture Video
Post-video Quiz
Assignment

Week 1
23 May Thursday: Read Alignment to Genomes
GoogleCollabNotebook
Slides
Lecture Video
Post-video Quiz
Assignment

Week 2
28 May Tuesday: Genome Assembly
GoogleCollabNotebook
Slides
Lecture Video
Post-video Quiz
Assignment

Week 2
30 May Thursday: Typing, AMR databases
GoogleCollabNotebook
Slides
Lecture Video
Post-video Quiz
Assignment

Week 3
4 June Tuesday: Genome Annotation, PathogenWatch
GoogleCollabNotebook
Slides
Lecture Video
Post-video Quiz
Assignment

Week 3
6 June Thursday: Phylogenetics, Surveillance
GoogleCollabNotebook
Slides
Lecture Video
Post-video Quiz
Assignment

Any reuse of the course materials, data or code is encouraged with due acknowledgement.

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License

This work is licensed under a Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).