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 evolutionary 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 over a one week period in November 2024.

This year, the workshop runs from November 4th 2024 - November 8th. There are two sessions a day, from 10am to Noon and from 2pm to 4pm.

The course will be run in person on the UBC campus in Biological Sciences building Rm 2139.

Instructors

Tom Booker & Bernadette Johnson

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.

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 1 Broad introduction: Scope of course, goals, overview of technology and bioinformatics
• Topic 2 Programming Basics
• Topic 3 Sequence Data
• Topic 4 Genome Assembly
• Topic 5 RNAseq + differential expression analysis
• Topic 6 Alignment: algorithms and tools
• Topic 7 SNP and variant calling
• Topic 8 Filtering variants
• Topic 9 Analysis of genomic data
• Topic 10 Optional Catch up & Work on assignment

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
• Topic Y Phylogenetic analysis

Evaluation

Your mark will reflect participation in class (discussions and lab exercises etc) as well performance on a final assignment. The breakdown is 80% of your mark will come from participation and 20% from the assignment.

Assignments

At the end of the week you will be given details of an assignment in class that combines different aspects of the work you’ll do throughout the week.

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) 2024 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