Additional Bioinformatics and Genomic Epidemiology Learning Resources

While each section of this course has introduced learning resources, some don’t fit into any of the specific topics, so are gathered here.

• Awesome Bioinformatics Education - a curated list of resources for learning bioinformatics (with a focus on pathogen bioinformatics). The list is curated by Dr Lee Katz from the US CDC.

• An applied genomic epidemiology handbook - the free version of Allison Black and Gytis Dudas’ textbook on genomic epidemiology.

• Primer on Phylogenetics - search for “Primer” in the recordings of the PhyloSeminars

• Glittr - Git repositories with bioinformatics training material

Resources from the Course modules

To make it easier to find resources, here are the resources mentioned elsewhere on the course website.

Shell Resources

• Introduction to Bash Shell Scripting

• Advanced Bash Scripting Guide

• Introduction to Shell scripting and Intermediate Shell Scripting from Sambit Sinha

• What is the difference between the Bash operators [[ vs [ vs ( vs ((?

Conda Resources

• Introduction to Conda from The Carpentries

Nextflow Resources

• Introduction to Bioinformatics workflows with Nextflow and nf-core from The Carpentries

• Nextflow training

• Nextflow and nf-core Mentorships

R Resources

• R for Descriptive Statistics and Graphics

• Data Visualisation using ggplot

• R for applied epidemiology and public health

• Easy R Programming from STHDA

• Introduction to ggplot2

• Introduction to dplyr

• Introduction to tidyverse

• Data Explorer for Exploratory Data Analysis

• R for Data Science

Galaxy Resources

See the section on Galaxy

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