SNP discovery and genotyping using reduced-representation sequencing data

Course details

In this 16.5-hour course, participants will learn how to design, perform, and analyse the results of a genotyping-by-sequencing experiment. The course will cover the basic concepts of library preparation (RAD-like and MobiSeq) and sequencing, and the key aspects of SNP discovery and SNP calling.

Participants will get the chance to work hands-on with real datasets, using different bioinformatic tools (STACKS tool set). The aim of the course is to provide researchers with the necessary resources to obtain their variant files for population genomics, phylogenomics, and crop genetic improvement.

Language: Spanish.

Number of places available: 18.

Instructors: Rocío Esteban, Dr. Jorge Doña, and Antón Vizcaíno.

Target audience and requirements

Master students, early career researchers (pre-docs and post-docs), or senior researchers, either from Industry or Academia, interested in genotyping-by-sequencing. Please note that this is an introductory course and is not intended for researchers with experience in SNP discovery and genotyping analysis.

Basic skills in high-throughput sequencing are required. Researchers who are not familiar with high-throughput sequencing might want to consider signing up first to our introductory course. Basic use of UNIX-based command line is desirable.

Hands-on work will be performed in UNIX environments (Linux, Mac).

All participants should bring and use their own laptops.

Course program

10:00 - 11:30 Introduction to reduced-representation library preparation: RAD and MobiSeq methods STACKS - Parameter selection Variant analysis using R (part 1)
11:30 - 12:00 Coffee! Coffee! Coffee!
12:00 - 13:30 Data pre-processing and tools for SNP discovery and genotyping Practical session: STACKS (basic modules and parameter selection) Variant analysis using R (part 2)
13:30 - 15:00 Lunch Lunch Lunch
15:00 - 16:30 Practical session: data pre-processing and tools for SNP discovery and genotyping STACKS - Populations: loci filtering, Fstats, Outputs (phylip, VCF, genepop, structure) Practical session: varian analysis
16:30 - 17:00 Coffee! Coffee! Coffee!
17:00 - 18:00 STACKS - Basic modules Practical session: STACKS (populations) Closing session: your own project
18:00 - 20:00 Free time Free time Good bye!
20:00 - 22:00 Dinner Dinner and party



First edition 2019: July 3 - July 5.

Second edition 2019: November 20 - November 22.


The course will be held at Camping Los Manzanos. Los Manzanos is a singular and quaint place in the municipality of Oleiros (A Coruña, Galicia, Spain). It is located within walking distance of the picturesque XVI-century castle and the lively cafés in the village of Santa Cruz. Travellers who want to enjoy being near the sea, but not right on the sea itself, flock to this original campsite in the woods which is well-known for its restaurant and its sculptures and paintings by Julio Sanjurjo. A Coruña, one of the most beautiful cities in Northern Spain is only 12 km. away.

The easiest way to reach the venue from A Coruña airport is by taxi; alternatively, you may take the airport bus to A Coruña Bus Station and then take the bus line to Santa Cruz. Please do not hesitate to let us know if you need further information on how to get to Los Manzanos.


Course fee (including course materials and refreshments): 525 euros.

Course fee + accommodation and meals: 690 euros. This package includes accommodation in shared bungalows (2 or 4 people) with en suite bathroom (check in on Tuesday evening; check out on Friday morning) and meals (breakfast, lunch, and dinner) at the venue restaurant. The bungalows are equipped with bed linen and towels, TV, coffee maker, toaster, microwave oven, fridge, flatware, dishware, and heating. Additional accommodation options are available at an extra cost.

How to apply

If interested, please fill out our contact form and specify:

  • The course and edition you are interested in enrolling in.
  • The details of the paying institution (including VAT number).

The sign-up deadline is 30 days prior to the start of the course.

Please note that there is an 18 participant limit and applications will be accepted on a first-come, first-served basis.

A 10 participant minimum per course edition is required. If that minimum is not reached the edition will be cancelled and participants offered a different edition or a total refund.