Bioinformatics_Overview

PHAR5002

Delivered in Semester 1

Module 1: Fundamentals of Bioinformatics

VM login instructions

Site - GithubIO

Introduction to BASH

• Practical 1 - Intro to BASH 1
• Practical 2 - Intro to BASH 2
• Practical 3 - Intro to BASH 3

Read Alignment and Variant Calling

• Practical 4 - Read QC
• Practical 5 - Read QC Pt2 and Scripting
• Practical 6 - Read Alignment
• Practical 7 - Variant Calling

Module 2: Pathogens and Metagenomics

Introduction to Pathogen Genomics

• Practical 1 - Introduction to Pathogen Genomics

Bacterial Genome Assembly

• Practical 2 - Short-read Genome Assembly
• Practical 3 - Long-read Genome Assembly
• Practical 4 - Genome Assembly Quality Control

Command Line BLAST

• Practical 5 - Introduction to BLAST
• Practical 6 - BLAST Applications

Metagenomics

• Practical 7 - Metagenomics

Module 3: Reproducible Bioinformatics

Failing Loudly

• Practical 1 - Failing loudly 1

• Practical 2 - Failing loudly 2

• Practical 3 - Code comments
• Practical 4 - Hashes, diffs and versions

Module 4: Version Control

• Practical 1 - Git Intro
• Practical 2 - Git Advanced
• Practical 3 - GitHub Intro
• Practical 4 - GitHub Advanced

Other Course Materials

• Overview of file types