Prerequisites and Requirements¶

Technical Prerequisites¶

Essential Requirements¶

1. Computing Equipment¶

Laptop with at least 8GB RAM (16GB recommended)
Operating System: Linux or macOS preferred
Windows users must install Git Bash before the course
Reliable internet connection for downloading datasets and software

2. Basic Technical Knowledge¶

Basic understanding of Linux command-line tools
File navigation (cd, ls, pwd)
File manipulation (cp, mv, rm, mkdir)
Text viewing (cat, less, head, tail)
Familiarity with text editors (nano, vim, or similar)
Basic understanding of file systems and permissions

3. Scientific Background¶

Undergraduate-level biology or microbiology
Basic understanding of genetics and molecular biology
Familiarity with concepts of:
DNA sequencing
Bacterial genetics
Infectious diseases
Public health surveillance

Recommended (Not Required)¶

1. Programming Experience¶

Basic scripting in Python, R, or shell scripting
Experience with data analysis workflows
Version control with Git (we'll cover this in Day 1)

2. Bioinformatics Background¶

Previous experience with sequence analysis tools
Understanding of genomic file formats (FASTA, FASTQ, VCF)
Familiarity with biological databases

3. High-Performance Computing¶

Access to HPC resources (recommended but not essential)
Experience with job schedulers (SLURM, PBS)

Software Requirements¶

Pre-course Installation¶

Please install the following software before the course begins:

1. Git (All Operating Systems)¶

Linux: sudo apt install git or equivalent
macOS: Install Xcode Command Line Tools or use Homebrew
Windows: Download and install Git Bash from git-scm.com

2. Text Editor¶

Choose one of: - VS Code (recommended for beginners) - Sublime Text - Atom - Vim/Emacs (for advanced users)

3. SSH Client¶

Linux/macOS: Built-in terminal
Windows: Use Git Bash or Windows Subsystem for Linux (WSL)

Course-Provided Software¶

The following will be provided during the course:

Docker/Singularity containers with pre-installed bioinformatics tools
Nextflow for workflow management
Access to high-performance computing resources
Pre-configured analysis environments

Data Requirements¶

Practice Datasets¶

We will provide: - Curated training datasets for all major pathogens - Quality-controlled sequence data in standard formats - Reference genomes and databases - Example analysis outputs for comparison

Bring Your Own Data (Optional)¶

If you have your own datasets: - Raw sequencing data (FASTQ format) - Associated metadata (sample information, collection details) - Ethical approval for data sharing (if applicable) - Data should be <100GB total for practical analysis

Pre-course Preparation¶

1. Complete the Setup Guide¶

Follow our detailed Setup Guide to prepare your computing environment.

2. Review Basic Concepts¶

Refresh your knowledge of: - Basic microbiology and infectious diseases - DNA sequencing principles - File formats in bioinformatics

3. Practice Command Line¶

If you're new to command line: - Complete an online tutorial (e.g., "Command Line Crash Course") - Practice basic file operations - Get comfortable with navigating directories

4. Test Your Setup¶

Verify Git installation: git --version
Test SSH connectivity (instructions will be provided)
Ensure you can create and edit text files

Accessibility and Support¶

Technical Support¶

Pre-course: Contact instructors for setup assistance
During course: Dedicated technical support available
Post-course: Community forum for ongoing questions

Accommodations¶

Please inform instructors of any: - Accessibility requirements - Dietary restrictions (for course meals) - Special technical needs

Language Support¶

Course materials are in English
Instructors can provide support in multiple languages
Translated resources available for key concepts

Questions?¶

If you have questions about prerequisites or setup:

Check the Troubleshooting Guide
Contact the course coordinators
Join our pre-course Q&A sessions (dates TBD)