PATHOGEN GENOMICS WORKSHOP

Aga Khan University, Karachi, Pakistan

August, 2022

https://bit.ly/pathogen22

Egon A. Ozer, MD PhD ([email protected])
Ramon Lorenzo Redondo, PhD ([email protected])

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Table of Contents

Part 1: Computational Resources

Preparing your computer for bioinformatics

Introduction to command line navigation

Data transfer: FTP, rsync, wget

Installing and managing software: Conda, GitHub, and Docker

Bash loops and basic automation

Part 2: Next Generation Sequencing

Overview of study design and sample collection

Introduction to Next Generation Sequencing

Introduction to sequence data and file types

Navigating the NCBI sequence database & data deposition

Quality control and trimming of sequencing reads

Sequence assembly

Genome annotation

Part 3: Variant Discovery and Phylogenetics

Reference-based sequence alignment and variant calling

Introduction to phylogenetics

Phylogenetics methods and theory

Multiple sequence alignment

Phylogenetics software and pipelines

Part 4: Phylogenetics and Data Visualization

Phylodynamics

Phylogeography

Phylogenetic data visualization and annotation

Introduction to R programming for statistical analysis and visualization (ggtree)

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