BBSRC STARS Bioinformatics Winter School

Monday, March 13, 2017 - 09:00 to Friday, March 17, 2017 - 17:00



The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK

Application deadline:

Monday 16 January 2017 noon


12 (selection of applicants)

Registration fee:

£ 0 (this includes refreshments and a course dinner, but no lunches and accommodation)


Bert Overduin

The aim of this Winter School is to provide comprehensive training in both the theory and practice of second- and third-generation sequencing bioinformatics. After a general introduction to bioinformatics and sequencing technologies, we will teach the necessary Linux skills, and then cover a range of popular analysis protocols for the analysis of second- and third-generation sequencing data, including new long-read technologies such as Oxford Nanopore and PacBio. To ensure that attendees can use what they have learned when they return to their host institution, each attendee will, as part of the Winter School, be provided with two hours' worth of follow-up meetings with Edinburgh Genomics’ dedicated analysis team. The EG analysis team has experience of all areas of second- and third-generation sequencing data analysis. Attendees are free to use these hours in any way they see fit. Ideally this should lead to analysed datasets, ready for publication and/or further downstream analysis.
Instructors (subject to change)
Sujai Kumar (Bioinformatician, The University of Edinburgh)
Dominik Laetsch (Bioinformatician, The University of Edinburgh)
Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics)
Judith Risse (Bioinformatician, Wageningen University, The Netherlands)
Rob Stewart (Bioinformatician, The Roslin Institute)
Urmi Trivedi (Bioinformatician, Edinburgh Genomics)
Frances Turner (Bioinformatician, Edinburgh Genomics)
Mick Watson (Director of ARK-Genomics & Research Group Leader, The Roslin Institute)

Workshop format

The workshop consists of presentations, demos, and hands-on tutorials.

Who should attend

Undergraduates, PhD students, postdoctoral researchers, and independent researchers who are using second- or third-generation sequencing in their research and who want to be able to analyse their data themselves.


A general understanding of molecular biology and genomics, and elementary skills in computer usage are required. Preference will be given to applicants who already have second- or third-generation sequencing data that are ready to be analysed.


Everyone can apply to attend this workshop, but priority will be given to BBSRC funded delegates (e.g. BBSRC PhD students and researchers funded on BBSRC grants) and delegates from UK companies.

Covered topics (subject to change!)

Biological databases
The Ensembl Genome Browser
Introduction to second- and third-generation sequencing technologies
Introduction to Linux
Quality control and data-preprocessing
Mapping to a reference
Mapping quality control
Visualisation of mapped reads
Differential gene expression analysis
Variant calling
Genome assembly
Long read bioinformatics

This workshop is funded by BBSRC Strategic Training Awards for Research Skills (STARS) grant BB/N019636/1