Genomic sequencing is used in a multitude of environmental applications, from the monitoring of rare and overlooked species using metagenomics, to detecting responses to climate change using population genomic sequencing. This two week intensive course will provide a practical introduction to ecological genomics, covering the types of wet lab methods (DNA extraction, library preparation and next generation sequencing) and bioinformatic analyses (data QC, genome assembly, phylogenetics) necessary to go from samples to sequence to results. Participants will track a single sample through all stages of the workflow, learning practical skills at each stage. The work will take place at Edinburgh Genomics, using cutting edge genomic equipment, with sequencing using nanopore to obtain results in real time. 

After completing the workshop, users should be able to: (1) prepare their own samples and libraries for genomic sequencing, (2) perform bioinformatic analyses of next generation sequencing data, (3) apply their skills to other sequencing methods and analysis problems. 

The course is centered on the example application of using genomics for species identification. Participants will be provided with a sample of unknown identity at the start of the course, which will be used in each stage of the genomics workflow. The analysis results generated later in the course will reveal the species’ identities. We will use plant samples collected around King’s Buildings campus, though the principles taught apply to any organism and the course emphasizes transferable skills in genomics and bioinformatics.

Dates:

Wet lab component: 24th April - 26th April

Bioinfomatics component: 3rd - 5th May

9.00am - 5.00pm

Venue:

Edinburgh Genomics, Ashworth Laboratory (ground floor), The Kings Buildings Campus, Charlotte Auerbach Road, EH9 3FL

Three travel grants per course, of £500 each, will be available for those travelling from outside of Edinburgh. Please fill in the relevant question on our application form to tell us if this is you!  

Places:

12 for each workshop

Application deadlines: Friday 10th March. Applicants will be notified within 2 weeks of the closing date whether they have secured a place.

Registration fee:

This course is funded by the Natural Environment Research Council (NERC) and is therefore free to attend for eligible candidates. 

Please note that in order to inssure attendance there will be a penalty charge of £200 levied against anyone who cancels the course within five days of the start date without good reason. 

Information:

Contact our training team

Instructors

Alex Twyford, Javier Santoyo-Lopez, Urmi Trivedi, Nathan Medd, Robert Foster, Tim Booth, Heleen De Weerd

Workshop format

We will have three days of hands on wet lab practicals and demonstrations, followed by three days of bioinformatics presentations, tutorials, and discussions.

Who should attend

The course is aimed at beginners, though basic lab skills and some familiarity with using the command line would be advantageous. Priority will be given to NERC funded students and researchers, as well as researchers from under-represented groups and those with the greatest training needs, though everyone is welcome to apply.

Covered topics

 Note that the course is six days spread over a two week period, with a break in the middle for sequence data generation and QC.

Day 1 (Monday) : Introduction, background, DNA extraction

Day 2 (Tuesday): Nanopore library preparation

Day 3 (Wednesday): Library QC and sequencing

Break for sequencing (Thurs-Tues)

Day 4 (Wednesday): Introduction to the command line and data QC

Day 5 (Thursday): Genome assembly

Day 6 (Friday): Comparative genomics

APPLICATIONS CLOSED: SEE NEXT INSTANCE (JUNE 2023)