Comparative genomics (CMGN01)
29th April 2019 - 3rd May 2019£275.00 - £550.00
This course will introduce biologists and bioinformaticians to the field of comparative genomics. The course will give a deeper understanding on the advantages and disadvantages of each of approach in general to enabling an informed decision of study design for the participants for future studies and learn the cutting edge approaches to process state of the art data sets. Different techniques will be introduced to identify single nucleotide polymorphism (SNP) and structural variations (SVs) as well as the annotation of these variations and the assessment for their functional impact.
We will give a broad introduction on how to:
- Process short and long read data based on multiple NGS data sets including mapping and de novo assembly
- Detect SNP and Structural Variations using de novo assembly, short or long read mapping
- Assess the impact of the detected variations
- Perform population genetic analysis between multiple samples to obtain a deeper insight into these variants.
Furthermore, we will teach on how to install and manage these methods and give an introduction in Cloud computing. This will enable the participants to set up efficient pipelines on their own institutions. The course will conclude with the participants being aware of the state of the art approaches and a deepened knowledge to decide which study design is the optimal for future studies .
This workshop is primarily aimed at researchers and technical workers with a background in biology, biomedical research and bioinformatics. It is intended to give a first overview on bioinformatic approaches for small sample sizes up to population scale studies. Prior knowledge on how to operate and navigate on a command line Linux environment is a plus, but not essential. Some time during the course will be dedicated to work on specific problems involving participants data sets with a team of instructors from the Baylor College of Medicine and Uppsala University.
Venue – PR informatics head office, 53 Morrison Street, Glasgow, G5 8LB – Google map
Availability – 25 places
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3 ECT’s
Language – English
We offer COURSE ONLY and ACCOMMODATION PACKAGES;
• COURSE ONLY – Includes lunch and refreshments.
• ACCOMMODATION PACKAGE (to be purchased in addition to the course only option) – Includes breakfast, lunch, welcome dinner Monday evening, farewell dinner Thursday evening, refreshments and accommodation. Self-catering facilities are available in the accommodation. Accommodation is approximately a 6-minute walk from the PR informatics head office. Accommodation is multiple occupancy (max 3-4 people) single sex en-suite rooms. Arrival Sunday 28th April (between 5pm – 9pm) and departure Friday 3rd May (accommodation must be vacated by 9am).
To book ‘COURSE ONLY’ with the option to add the additional ‘ACCOMMODATION PACKAGE’ please scroll to the bottom of this page.
Other payment options are available please email firstname.lastname@example.org
Cancellation policy: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact email@example.com Failure to attend will result in the full cost of the course being charged. In the unfortunate event that PRinformatics must cancel this course due to unforeseen circumstances a full refund for the course will be credited. However PRinformatics cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.
The workshop will be structured with lectures explaining the theory of certain topics followed by practical’s covering this theory. Breaks will be at the instructors discretion. There will also be plenty of time for students to discuss their own problems and data.
Assumed quantitative knowledge
Students should have enough biological background to appreciate the examples and exercise problems, and have at least some interest in working with next generation sequence (NGS) data.
Assumed computer background
No programming or scripting experience is necessary, but some previous expertise using a Linux terminal and/or R will be most welcome.
IMPORTANT: If you have not used a Linux command line before, it is highly recommended that you complete at least one of the following brief primers shortly before arriving at the course:
Equipment and software requirements
A laptop/personal computer.
All examples will be run in a Linux environment on the cloud.
Students will use their own laptops to access the cloud, and need only to have R, RStudio, IGV, and some terminal software installed (e.g. Terminal for Mac, PuTTY, or similar).
R, RStudio, and IGV are supported by both PC and MAC and can be downloaded for free by following these links:
It is essential that you come with all necessary software and packages already installed.
UNSURE ABOUT SUITABLILITY THEN PLEASE ASK firstname.lastname@example.org
Meet at 43 Cook Street, Glasgow G5 8JN at approx. 17:00 onwards
Monday 29th – Classes from 09:30 to 17:30
Day 1: Intro + Assembly
Setting up and getting familiar with the system
Data types, technology overview
De novo assembly
Getting used to the environment
Manipulating read data (filtering, trimming, etc.)
Short vs. long read assembly
Subprocessing: QC, polishing of de novo assemblies
Tuesday 30th – Classes from 09:30 to 17:30
Day 2: Assembly quality + polishing ; RNA-Seq + short read mapping
How it works behind the scenes
Insight in short read mappers
Long read mapping
Wednesday 1st – Classes from 09:30 to 17.30
Day 3: SNP? + SVs detection (Assembly, Read based, phasing?)
Structural variation detection
Methods to detect SV
Current state of the art of technologies.
Short read based SV calling
Long read based SV calling
Assembly based SV calling
Comparing and filtering SVs
Annotation of SVs
Thursday 2nd – Classes from 09:30 to 17:30
Day 4: Larger analysis over multiple data set and assessment of mutations over FST
Evolutionary genetics of structural variation
Study design and sampling schemes
Descriptive (SNP & SV density)
PopGen (Fst, genetic diversity)
Friday 3rd – Classes from 09:30 to 16:00
Day 5: Summary and conclusion
Group discussions, final questions and overall summary (own data questions if time permits)