Exercises
PGIP 2025 • Population Genomics in Practice
Information
All exercise pages start with a callout block that provides information on how to setup the relevant Compute environment. The callout blocks are labelled with icons that indicate the type of environment ( PDC resource; local compute environment; online browser-based resource). Make sure to read these instructions before proceeding with the exercise itself. Some of the documents include a link to an external URL that hosts the actual exercise instructions.
Before proceeding, make sure to read Compute environment for information on how to prepare your working directory.
On self-assessment exercise blocks
Scattered throughout the documents are exercise blocks, with hidden answers, and, in some cases, hints. The exercises are for self-assessment of your understanding, but they are not mandatory.
Some of the exercises (labelled with the Linux penguin ) are related to the usage of the command line interfaces (CLI), and how to obtain information about what a program does. This is an essential skill when working in Linux/UNIX environments! These exercises can be skipped if you are an experienced Linux/UNIX user.
An example exercise is provided here:
The ls command is used to list the contents of a directory. What option provides a so-called long listing format?
Type ls --help to show the options to ls.
The -l option uses the long listing format, i.e., the command to use is ls -l.
Exercises
| Title | Description |
|---|---|
| Compute environment | Description of compute resources |
| Monkeyflowers dataset | Summary of Monkeyflower dataset from Stankowski et al. (2019) |
| Variant calling index | List of exercises |
| Variant filtering index | List of exercises |
| Recombination and linkage index | List of exercises |
| Genetic diversity index | List of exercises |
| Population structure index | List of exercises |