Hands on Workshop: Introduction to Bioinformatics

Intro to Bioinformatics - Monash SBS 2019

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Description

The purpose of this course is to provide graduate students with the theoretical knowledge and practical skills for the analysis of high throughput sequence data. The course will entail data retrieval and assembly, alignment techniques, variant calling, gene expression analyses, hypothesis testing, and population genomic and phylogenomic approaches. The course will be presented as a series of short lectures and lab exercises over a one week period during the mid semester break of the second semester.

Instructors

Dr. Kathryn Hodgins, Dr. Gregory Owens, Dr. Matt McGee, Dr. Sonika Tyagi

Format

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

Prequisites

Prior exposure to R and Unix command line is recommended. However, we will be running a crash course on command line the first day.

Lectures/tutorials

30 Sept 2019 – 4 Oct 2019 10am to Noon, 1pm to 3pm

Where

Room 144 (Digilabs), Building 17 School of Biological Sciences

Basic course structure

The course material is organized in several topics, with slides and coding examples.

To get up to speed on working with a Unix system, take a look at 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 Workshop overview & sequencing technology and approaches (Day 1 AM)

Lecture: Workshop overview and goals (Kay) Sequencing technology and approaches (Matt Tinning, NGS manager of AGRF) Tutorial: R intro (Sonika)
Topic 2 Command line introduction (Day 1 PM) Tutorial: Command line introduction (Damien)
Topic 3 Sequence file formats and quality control/trimming (Day 2 AM)

Lecture: Sequence file formats and quality control/trimming (Kay) Tutorial: QC GBS and RNAseq reads (Kay)
Topic 4 Sequence alignment (Day 2 PM)

Lecture: Alignment algorithms and tools (Greg) Tutorial: Alignment of NGS data (Greg)
Topic 5 Variant calling (Day 3 AM)

Lecture: SNP and variant calling (Greg) Tutorial: Call variants for NGS data (Greg)
Topic 6 Population genomics (Day 4 AM)

Lecture: Population genomics (Greg) Tutorial: Population genomics (Greg)
Topic 7 Population genomics and plotting in R (Day 4 AM)

Tutorial: Population genomics and plotting in R (Greg)
Topic 8 Phylogenetics (Day 3 PM) (Matt) - NOTE: Due to a scheduling conflict the Phylogenetics Topic will be Day 3 PM
Topic 9 Genome assembly (Day 5 AM) (Sonika)
Topic 10 RNAseq + differential expression analysis (Day 5 PM) (Sonika)

Obtaining all the files on this site

To access the course content offline, you may download an up-to-date snapshot archive of the site content from this location: https://github.com/khodgins/Bioinformatics_Introduction/archive/master.zip

But the recommended approach is to use git which tracks changes and supports incremental updates:

git clone https://github.com/khodgins/Bioinformatics_Introduction.git

If the course content changes, you can update your local copy by going into to the Bioinformatics_Introduction directory that was created by the previous command and invoking the command:

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

The license file is here

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