BBSRC STARS Bioinformatics Winter School


Date:

Early 2018

Venue:

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

Application deadline:

to be determined

Places:

12 (selection of applicants)

Registration fee:

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

Information:

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.


"Many thanks to BBSRC, Edinburgh Genomics, and all the trainers for such a great week. I am now confident in doing my PhD!" (March 2017)"


Instructors in 2017

Sujai Kumar (Bioinformatician, The University of Edinburgh)
Dominik Laetsch (Bioinformatician, The University of Edinburgh)
Ben Moore (Ensembl Outreach Officer, EMBL European Bioinformatics Institute, Hinton, Cambridge)
Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics)
Judith Risse (Bioinformatician, Wageningen University, The Netherlands)
Urmi Trivedi (Bioinformatician, Edinburgh Genomics)
Frances Turner (Bioinformatician, Edinburgh Genomics)

Speakers in 2017

Mark Blaxter (Professor of Evolutionary Genomics, The University of Edinburgh)
Karim Gharbi (Facility Manager Genome Science, Edinburgh Genomics)
Catherine Kidner (Senior Lecturer in Plant Evolution, The University of Edinburgh / Royal Botanic Garden Edinburgh)
Mick Watson (Professor of Bioinformatics and Computational Biology, 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.

Requirements

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.

Eligibility

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.


Time schedule 2017

Monday 13 March 2017

09:00 - 09:15 Welcome Bert Overduin
09:15 - 10:15 Introduction of participants Participants
10:15 - 10:30 Coffee break
10:30 - 11:15 "What can bioinformatics do for you" (t) Mick Watson
11:15 - 12:30 Introduction to Linux (t/h) Bert Overduin
12:30 - 13:30 Lunch break
13:30 - 15:15 Introduction to Linux (t/h) Bert Overduin
15:15 - 15:30 Coffee break
15:30 - 17:00 Introduction to Linux (t/h) Bert Overduin
18:00 - ??:?? Pub social

Tuesday 14 March 2017

09:00 - 09:30 Biological databases (t) Bert Overduin
09:30 - 10:30 Ensembl Genome Browser (t/d/h) Ben Moore
10:30 - 10:45 Coffee break
10:45 - 12:30 Ensembl Genome Browser (t/d/h) Ben Moore
12:30 - 13:30 Lunch break
13:30 - 14:30 Ensembl Genome Browser (t/d/h) Ben Moore
14:30 - 15:45 “Introduction to modern DNA sequencing technologies” (t) Karim Gharbi
15:45 - 16:00 Coffee break
16:00 - 17:00 Tour of the Edinburgh Genomics sequencing facility Karim Gharbi

Wednesday 15 March 2017

09:00 - 10:30 Quality Control and data pre-processing (t/h) Urmi Trivedi
10:30 - 10:45 Coffee break
10:45 - 12:30 Mapping to a reference (t/h) Urmi Trivedi
Mapping quality control (t/h) Urmi Trivedi
12:30 - 13:30 Lunch break
13:30 - 15:15 Visualisation of mapped reads (t/h) Urmi Trivedi
Estimating gene count (t/h) Urmi Trivedi
15:15 - 15:45 Introduction to R (h) Bert Overduin
15:45 - 16:00 Coffee break
16:00 - 17:00 “The hidden history of symbiosis between Wolbachia and filarial nematodes: mining genomes for fossils of association” (t) Mark Blaxter

Thursday 16 March 2017

09:00 - 10:30 Differential expression analysis (t/h) Frances Turner
10:30 - 10:45 Coffee break
10:45 - 12:30 Differential expression analysis (t/h) Frances Turner
Functional analysis (t/h) Frances Turner
12:30 - 13:30 Lunch break
13:30 - 15:45 Variant calling, filtering, and annotation (t/h) Bert Overduin
15:45 - 16:00 Coffee break
16:00 - 17:00 “The genomic legacy of Victorian plant hunters” (t) Catherine Kidner
18:30 - ??:?? Course dinner

Friday 17 March 2017

09:00 - 10:30 Short read assembly (t/h) Sujai Kumar
10:30 - 10:45 Coffee break
10:45 - 12:30 Assembly QC (t/h) Dominik Laetsch
12:30 - 13:30 Lunch break
13:30 - 15:15 Using longreads for scaffolding of short reads and hybrid de novo assembly (t/h) Judith Risse
15:15 - 15:30 Coffee break
15:30 - 16:30 Using longreads for scaffolding of short reads and hybrid de novo assembly (t/h) Judith Risse
16:30 - 17:00 Troubleshooting or “What can go wrong” (t) Sujai Kumar, Dominik Laetsch, Judith Risse

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