RADCamp Latin America 2026 Part II (Bioinformatics) - Day 1 (AM)
Overview of the morning activities:
- RADCamp Part II Learning Objectives
- Lecture: Intro to RADSeq (Brief)
- Exercise 0: HPC system access & setup (Isaac)
- Exercise 1: Intro to FASTQC format and quality control (Isaac)
- Coffee Break (10:30-10:50)
- Lecture: ipyrad history, philosophy and workflow (Deren)
- Exercise 2: ipyrad CLI assembly of simulated data
- Exercise 3: Assemble mystery data
- Break for Lunch (12:45-1:30)
Learning objectives.
By the end of this workshop you will gain experience with:
- More efficiently use tools for reproducible bioinformatics (unix, jupyter, ipyrad, etc)
- Using HPC infrastructure to run genomic analyses
- Understanding how RAD sequence data is related to the methods we performed in the lab to create it
- Assembling a RAD-Seq dataset with ipyrad
- Understanding and dealing with missing data in RAD-seq analyses
- Running several evolutionary analysis tools on RAD-seq data
Brief intro to RADSeq
Lead: Deren
- Slides: Introduction to RAD and the terminal
- History of RAD-seq.
- When to use RAD-seq and comparison to alternatives.
- Brief introduction to the command-line and filesystems.
Coffee break (10:30-10:50)
ipyrad history, philosophy, and workflow
Lead: Deren
ipyrad CLI simulated data assembly
Lead: Isaac
Exercise: ipyrad command line assembly with simulated data
Assemble mystery data
Practice the ipyrad2-classic assembly workflow using a mystery dataset and also the Seadragon data (if time).