GenEpi-BioTrain - Training Materials on Genomic Epidemiology and Public Health Bioinformatics - Bridging the gaps: All participants

File File Welcome/Intro ECDC

Overview

Page Page Target audience

Page Page Structure

Page Page Training objectives

File File Possible course schedule

Page Page Background and acknowledgements

Training Materials

Label Label PRE-COURSE ACTIVITIES

File File Online orientation session for participants (2 weeks in advance)

Page Page Create user-account on ENA

File File Unix Handout

Label Label THEME 1 - GETTING STARTED IN BIOINFORMATICS

Page Page Module 1.1 Course introduction (outline)

Folder Folder Module 1.1 materials

Page Page Module 1.2 Introduction to Linux and Bash (outline)

Folder Folder Module 1.2 materials

Page Page Module 1.3 Getting started with python (outline)

Folder Folder Module 1.3 materials

Page Page Module 1.4a Advancing in programming (outline)

Folder Folder Module 1.4a materials

Page Page Module 1.4b Coding best practice 2023 (outline)

Folder Folder Module 1.4b materials

Label Label THEME 2 - SEQUENCING AND ASSEMBLY

Page Page Module 2.1 Sequencing and raw-data QC (outline)

Folder Folder Module 2.1 materials

URL URL Quality Control of Raw read data

Page Page Module 2.2 Introduction to genome assembly (outline)

Folder Folder Module 2.2 materials

Page Page Module 2.3a Short-read genome assembly and QC

Folder Folder Module 2.3a materials

Page Page Module 2.3b Reference-based assembly (SARS-Cov-2/Influenza) (outline)

Folder Folder Module 2.3b materials

Page Page Module 2.4 Long-read and hybrid de novo genome assembly (outline)

Folder Folder Module 2.4 materials

Label Label THEME 3 - GENOME ANALYSIS AND SHARING

Page Page Module 3.1 Blast, in silico MLST and gene annotation (outline)

Folder Folder Module 3.1 materials

Page Page Module 3.2 - Getting started with phylogenies (outline)

Folder Folder Module 3.2 materials

Page Page Module 3.3a - Pathogen-wave oriented analyses 2023 (outline)

Folder Folder Module 3.3a materials

Page Page Module 3.3b - Pathogen-wave oriented analyses 2024 (outline)

Folder Folder Module 3.3b materials

Page Page Module 3.3c - Pathogen-wave oriented analyses 2025 (outline)

Folder Folder WGS-based detection of antimicrobial resistance (AMR) in bacteria

Folder Folder Tuberculosis profiling

Page Page Module 3.4 - Data sharing (outline)

Folder Folder Module 3.4 materials

Page Page Module 3.5 Online tools for genetic analysis (outline)

Folder Folder Module 3.5 materials

Label Label THEME 4 - PIPELINE DEVELOPMENT AND AUTOMATION

Page Page Module 4.1 Pipeline development (outline)

URL URL Bacterial Genome Assembly - Advanced (For the Independent coders)

URL URL Bacterial genome assebmly - Intermediate (Exercises with a helping hand)

URL URL Bacterial Genome Assembly - VERY Basic (Exercise in copy pasting)

Folder Folder Module 4.1 Old materials

Page Page Module 4.2 Automation – going large-scale (outline)

Folder Folder Module 4.2 materials

Label Label WHAT'S NEXT?

Page Page Module 5.1 - What's next (outline)

File File outlook continued learning

Folder Folder Additional Resources - Scripts developed by trainers

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