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Best practices for training in Next Generation Sequencing Analysis

Best practices for training in Next Generation Sequencing (NGS) Analysis

Date: 13-14 January 2015

Venue: Centre for Mathematical Sciences, Cambridge, UK

Organizers: , University of Cambridge (contact to discuss content), Myrto Kostadima, University of Cambridge and Vicky Schneider, The Genome Analysis Centre (TGAC). Administrative support: , TGAC (contact for administrative enquiries) and Cathy Hemmings, University of Cambridge

Workshop description and aims:

This workshop will bring together trainers involved in teaching NGS analysis to life scientists and give them the opportunity to work on developing a unified collection of training materials, tailored to different audiences and updated collaboratively.

This will be primarily a hands-on workshop, where participants will be asked to share their materials prior to the event and, during the actual workshop, work together to integrate materials, upload them to a common repository, agree on common descriptors and discuss learning assessment methods.

At registration, we will ask participants to follow these instructions:

1) Pick an NGS application for which they have developed training materials, choosing between: RNA-seq, ChIP-seq or WGA. If none of these three are applicable, please contact Gabriella Rustici.

2) Pick a module from the following:
a) introduction to NGS applications/data formats/QC
b) mapping or assembly (including de novo)
c) application dependent-experimental design/statistics
d) application dependent-downstream analysis
e) data visualization
f) all of the above (for materials covering an entire pipeline)

For each chosen module, each participant will be asked to bring the following:
a)  example datasets
b)  module description: learning objectives, target audience, software requirements etc.
c)  presentations
d)  interactive exercises
e)  practicals/code for different audiences: introductory/intermediate/advanced
f)   assessment exercises (e.g. quizzes)
g)  test run scripts, if available

All materials will be shared prior to the workshop. We will set up a suitable place for sharing materials and send instructions in due course. If materials are already available online, we will ask for the link to the materials’ location. We will also collect participants’ selection criteria and examples of pre-course exercises, if applicable.

If there is a particular topic that participants would like to discuss during the course (e.g. something that you have done in the classroom and that has worked particularly well), let Gabriella Rustici know. Participants’ presentations will be kept short to maximize the time spent working on training materials.


Draft timetable

Day 1 (9:00 - 17:00)

Welcome and introductions

How do we select course participants and what are the most important eligibility criteria?

What pre-course work is needed to maximize learning outcomes?

Coffee break

Group work by application/module


Group work by application/module (cont.)

Day 2 (9:00 - 17:00)

Group work by application/module (cont.)


Presentation/discussion of the groups’ work

Assessment methods - how do we measure learning outcomes?


Registration link (by invitation only)

Details of how to register can be found here



This workshop received contributions from the COST action SeqAhead and Elixir UK.


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