Carpentries-style computer practical for Molecular Epidemiology of Infectious Diseases

less than 1 minute read


Tutorial for the computer practical

As a Carpentries instructor and trainer I am familiar with the Carpentry lessons, especially with the Data Carpentry Genomics lesson for which I am one of the maintainers of the shell-genomics episode. However it was my first time using the new lesson template for university course lessons. These lessons have been given already in 2016 but needed an update. Here is the link to the new lessons.

The intended target audience for this computer practical are phD students in epidemiology. They probably do not have much experience on the command line but are likely familiar with statistical programming e.g. in R. I used part of the shell-genomics and the wrangling-genomics episodes to introduce the shell and tool usage and then went on to work with the dataset and a bioinformatics workflow.

The computer practical uses data from this publication and is centered around confirming or disputing suggested transmission events with evidence from the genomic data.