Bioinformatics for Evolutionary Biology and Conservation

The purpose of this course is to provide graduate students with the theoretical knowledge and practical skills for the analysis of high throughput genomic sequencing data. The course will involve data retrieval and genome assembly, sequence alignment, variant calling and data analysis. The course will be presented as a series of short lectures and lab exercises during the week of November 3rd 2025. There is a session the week prior to the workshop (October 28th 2025) to go over UNIX and to introduce the structure of the course. There is also a final session two weeks after the class is finished to go over the assignment (November 28th).

During the week of the workshop there are two sessions a day, from 10am to Noon and from 2pm to 4pm.

The locations of class are detailed on Workday. I’ll also send round reminders during the week of the class.

Instructor

Tom Booker (contact info available from UBC’s website)

Format

A mix of lecture and lab exercises, running in a 2-hour block.

The course material is organized in several topics, with slides and coding examples given in each. Typically we have a lecture for the first half of each class and a practical session for the second. Usually we cover one topic per lecture, but we leave plenty of room for discussion and extension on each topic.

Prequisites

Students should have a good grasp of genetics and genomics and have fair computer literacy (e.g. know what RAM, threads and servers are).

The purpose of this workshop is to demonstrate the fundamentals of bioinformatic analysis. We will need to use the command line throughout the week, so it would be highly prefereable if participants had taken part in an introduction to the Unix command line workshop before participating in this one. To get up to speed on working with a Unix system, we recommend having taken the equivalent of Introduction to the Command Line for Genomics from Data Carpentry.

• Software Carpentry Tutorial

For a handy reference of common Unix commands check out the unix help file. There are some resources there that will help you find the specific command you need for each task.

Syllabus

• Topic 0 Programming Basics (October 28th)

• Topic 1 Broad introduction: Scope of course, goals, overview of technology and bioinformatics
• Topic 2 Sequence Data
• Topic 3 Genome Assembly
• Topic 4 RNAseq + differential expression analysis
• Topic 5 Alignment: algorithms and tools
• Topic 6 SNP and variant calling
• Topic 7 Filtering variants
• Topic 8 Analysis of genomic data

Extras

In previous years, there have been other topics that were included in the workshop as well as brief tutorials on other aspects of bioinformatics. In this section we include the slides and materials for those topics for those who are interested:

• Topic X Phylogenetic analysis

Evaluation

After the last session we will sit down to go over how you felt about your performance in class. We will both write down what we feel you earned in the class. The final grade will be determined from the grades we both assigned. The grade I will assign will reflect participation and effort in class (discussions and lab exercises etc) as well performance on the final assignment.

Chinook

In this workshop we make use of simulated datasets for all of the tutorials and demonstrations. The simutions model a populations of Chinook Salmon living in the Fraser River in Southern British Columbia. We use a population genetic simulation modelling local adaptation to varying environmental conditions. These simulations are used to generate DNA and RNA sequence data that we use to demonstrate bioinformatic principles and give workshop participants experience using standard tools. The biggest benefit to using simulations is that we can compare bioinformatic estimates to a ground truth, which is not possible when using real data.

The GitHub page for Chinook is here: https://github.com/TBooker/Chinook

Obtaining all the files on this site

You may use your internet connection to browse this site, or you may download the entirety of the files on the site in one constantly updated zip archive here

This method dosesn’t require git, however, you’ll have to manually update the files this way (by downloading the whole repo again).

To obtain to all the files via git, type:

git clone https://github.com/UBCForestryBioinformatics/UBCForestryBioinformatics.github.io To update the all the files at any point in the future, change to the directory that was created by the previous command and type:

git pull Use and modification of these resources You may use any of the materials provided here, and modify them in any way, provided there is appropriate attribution according the license found below and included with this project.

License and Copyright

This program is distributed under the MIT (X11) License, which should be distributed with the package. If not, it can be found here: http://www.opensource.org/licenses/mit-license.php

Modified work (c) 2025 Tom Booker

This workshop has been evolving since 2015 when it was first set up by researchers in the BRC at UBC.

About this site:

This site is powered by GithubPages, and the code backing it is here: [https://github.com/UBCForestryBioinformatics/UBCForestryBioinformatics.github.io