Welcome!
This is the official website for the RADseq workshop following the XI Congreso Latinoamericano de Herpetologia in Quito, Ecuador, sponsored by QCAZ @ PUCE. Virtual Machine support is provided by Lab7. The workshop will take place in the Sala de Uso Múltiple on the first floor of the Biology Building from July 31 until August 5 of 2017. We will cover theory and experimental design of RADseq projects as well as laboratory methods and bioinformatic pipelines.Before the workshop, please complete the following three tasks, in this order:
1. Fill out this pre-course survey2. Install the virtual machine as described in the installation instructions page
3. Complete lessons 1-3 of this software carpentry course on bash/shell, unless you are certain that you feel comfortable in the shell environment.
Syllabus and Materials
| Day | Time | Topic | Lesson Type | Instructor(s) |
|---|---|---|---|---|
| Monday, July 31 | Morning | Introduction | Discussion | Becca, Pati, David |
| Monday, July 31 | Morning | To RAD or not to RAD | Lecture | Pati |
| Monday, July 31 | Afternoon | RADseq Study Design | Lecture | Becca |
| Monday, July 31 | Afternoon | RADseq Wetlab Overview | Lecture | Becca |
| Monday, July 31 | Afternoon | ddRAD Wetlab Protocol | Lecture | Pati |
| Tuesday, August 1 | All day | Lab protocol design | Interactive | Pati |
| Wednesday, August 2 | Morning | RADseq Pipelines Overview | Lecture | Becca |
| Wednesday, August 2 | Morning | Getting Started in Shell | Interactive | Becca |
| Wednesday, August 2 | Afternoon | 2bRAD Data Pipeline | Interactive | Becca |
| Wednesday, August 2 | Extra | ddRAD Data in iPyrad | Interactive | Becca |
| Thursday, August 3 | Afternoon | ddRAD data in stacks | Interactive | Pati |
| Friday, August 4 | Morning | Stacks, filtering, and missing data | Lecture | Pati |
| Friday, August 4 | Afternoon | ddRAD Data in AftrRAD | Interactive | David |
| Saturday, August 5 | Morning | Case Studies with RADseq | Lecture | David |
| Saturday, August 5 | Morning | Case Studies with RADseq Using R | Lecture / Interactive | Pati |
| Saturday, August 5 | Afternoon | Course wrap-up and Q & A | Discussion | Pati, Becca, David |
The Virtual Machine we use in this course is provided by Lab7 Systems, a company in Austin, TX that offers software solutions for life science labs. Their core commercial software solution is the Lab7 Enterprise Science Platform (ESP), which is the first, complete sample-to-answer software platform for integrating and managing data-intensive lab operations (think [wet-lab] LIMS + informatics + reporting all in one system). BioBuilds is their curated collection of pre-built open-source bioinformatics tools that aims to reduce the headaches associated installing and maintaining these tools (e.g., dependency hell and quirky build systems). It’s free for anyone to download and use, but Lab7 offers support contracts for anyone who needs additional technical support, packages with licensing constraints, or support deploying these tools in regulated environments (e.g., clinics). Lab7 also has other offerings, including the Lab7 Genomic Cloud and consulting.