README.md

July 31, 2026 · View on GitHub

Welcome to the Biodiversity Genomics course held in Bogotá, Colombia in July 2026

For the course taught in July 2024 at IKIAM University in Tena, Ecuador, see the folder 2024_Ecuador. For the course taught in November 2025 at CONISET in Mendoza, Argentina, see the folder 2025_Argentina.

This course is taught by Karin Näsvall, Nicol Rueda, Fernando Seixas, and Joana Meier from the Wellcome Sanger Institute and by Gustavo Silvia Arias (Instituto de Ciencias Naturales, Universidad Nacional de Colombia - sede Bogotá). Some of the course material is based on the speciation genomics course by Joana Meier and Mark Ravinet.

The course website showing logistics and useful information about Bogotá is here.

Course materials

Sunday:

  • Slides basic introduction to unix and the command line
  • Exercise on how to use the command line
  • Exercise on more use of the command line
  • Exercise for more advanced users (awk, variables, arrays, writing a bash script)

Day 1 (Monday):

  • Slides introducing the course and biodiversity genomics
  • Slides Raw reads and quality control
  • Exercise on exploring Illumina reads and visualising the quality with fastqc which uses these input files
  • Exercise on filtering and trimming reads

Day 2 (Tuesday):

  • Slides about mapping reads to a reference genome
  • Exercise on aligning reads to a reference genome
  • Slides on variant and genotype calling
  • Exercise on variant and genotype calling

Day 3 (Wednesday):

Day 4 (Thursday):

Day 5 (Friday):

  • Slides on detecting selection at long time-scales
  • Exercise on detecting selection at long time-scales
  • Slides on comparative genomics
  • Exercise on genome synteny
  • Slides providing a summary of the course, further learning opportunities and an introduction to biodiversity genomics initiatives in Latin America

Advanced materials:

Learning more

Speciation genomics course website

https://speciationgenomics.github.io/ contains many more tutorials, including topics not covered here, such as demographic modeling, haplotype-based tests for selection, advanced unix and R tutorials, simulating data with SliM, etc.

Speciation and population genomics workshop

Workshop website contains many useful tutorials that are quite advanced, including machine learning and pangenomics.

Course material of the genomics workshop in Cesky Krumlov

Workshop website scroll down to the slides and exercises

Genome assembly tutorial by Marcela Uliano-Silva & João Ferreira

https://eukaryotic-genome-assembly.github.io

tidypopgen (R package for population genomics):

website

For RAD or UCE data

If you have short-read data for only a subset of the genome because you used a reduced-representation technique (e.g. RAD or UCE), most of the tutorial will still be relevant. For RAD or UCE data you do not necessarily need a reference genome, unless you want to run the genome scans for finding regions with high differentiation or introgression. If you have RAD (restriction-enzyme associated DNA) data, you can either follow the steps in our tutorial with mapping reads to a reference genome or if you do not have a reference genome, you can do a de novo assembly, i.e. make your own reference for just the RAD loci. The most widely used tool for RAD data analysis is STACKS or if you have a phylogenetic dataset with many species, we can recommend ipyrad. If you are working with polyploids, check out polyRAD. If you have UCE (ultra-conserved elements) data, have a look at this website for guidance.

Pipelines used at the Wellcome Sanger Institute for genome assembly and curation

https://pipelines.tol.sanger.ac.uk Pipelines including on Genome assembly, Genome curation with Pretext, Quality assessment of genomes, Metagenome assembly But also pipelines for read mapping, Variant calling,

Wetlab protocols used at the Wellcome Sanger Institute

Publication describing the methods and detailed protocols for lots of lab steps and different taxonomic groups on protocols.io.

Publications we recommend:

Introduction to Unix

Reviews on biodiversity genomics:

  • Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation van der Heijden et al. 2024
  • Genomic evidence reveals three W-autosome fusions in Heliconius butterflies Rueda et al. 2024

Papers or manuals for some of the tools mentioned in this course:

Reviews on phylogenomics

Reviews on speciation

Reviews or examples about introgression

Reviews or examples on chromosome evolution

Review on next-generation sequencies technologies

Population genomic diversity and divergence statistics

  • Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography Van Belleghem, et al., 2017
  • Complex modular architecture around a simple toolkit of wing pattern genes Van Belleghem, 2018