SNP discovery and genotyping using reduced-representation sequencing data course
In this 18-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 (AgriSeq Targeted Genotyping by Sequencing, 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: English or Spanish.
Number of places available: 12.
Instructors: Jaime Imaz, Paula Ramilo, 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.