Welcome!
This is the official website for the "Genomics of Biodiversity: a crash course on why and how" prior to the Segundo Congreso Latinoamericano de Biogeografía in Quito, Ecuador, sponsored by USFQ.WORKSHOP SUMMARY: Next Generation Sequencing has revolutionized biodiversity studies. As a consequence, biodiversity scientists must learn basic proficiency in computer programming in order to wrangle these new, enormous datasets. In this workshop we first aim to explore the kinds of questions that can be addressed with high-throughput sequencing as well as how the nature of the data influences the kinds of questions to be asked. We will then delve deeper into RADseq approaches, which have become widely used in ecological and evolutionary studies of non-model organisms. We include several interactive sessions that take us all the way from dealing with raw RADseq data to running it through the stacks assembly pipeline, inferring phylogenies with RAxML-ng, and building PCAs from SNP matrices in R. We encourage students to sign up that plan to use such methods in the immediate future.
The workshop will take place in the Newton Building on USFQ Main Campus in room N-212 from 09:00-18:00 on 5 August 2019.
Before the workshop, please complete the following three tasks:
1. Fill out this pre-course survey2. Complete lessons 1-3 of this software carpentry course on bash/shell, unless you are certain that you feel comfortable in the shell environment.
3. Complete lessons 4-6 of this software carpentry course on R, unless you are certain that you feel comfortable in the R environment.
Syllabus and Materials
| Time | Topic | Lesson Type | Instructor(s) |
|---|---|---|---|
| 09:00-10:15 | Introduction to Genomics: why and how? | Discussion | Becca & Pati |
| 10:15-11:00 | Getting Started with Raw Illumina Data | Interactive | Becca & Pati |
| 11:00-11:15 | Coffee Break | ||
| 11:15-13:00 | demultiplexing and genotyping in stacks | Interactive | Becca & Pati |
| 13:00-14:00 | Lunch | ||
| 14:00-15:00 | exporting and filtering matrices | Interactive | Becca & Pati |
| 15:00-16:00 | building a SNP phylogeny | Interactive | Becca |
| 16:00-16:30 | Coffee Break | ||
| 16:30-17:00 | quick popgen analyses in R | Interactive | Pati |
| 17:00-18:00 | final Q&A session | Discussion | Becca & Pati |