Workshop Structure

This Workshop is devided in 2 lessons:

Pangenome Analysis in Prokaryotes
Genome Mining in Prokaryotes

Here you can found instructor notes for all of those lessons.

General notes for the whole workshop

Technical tips and tricks

The parent directory of everything that we will be using during the lesson is /home/dcuser/dc_workshop❓. At the beginning of the workshop make sure it looks like this:

FIXME: tree command of the dc_workshop❓ folder. 💢

Installation

This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. See the Setup page for complete setup instructions. If you are teaching these lessons, and would like an AWS instance to practice on, please contact team@carpentries.org.

Common problems

✳️ This workshop introduces an analysis pipeline, where each step in that pipeline is dependent on the previous step. If a learner gets behind, or one of the steps doesn’t work for them, they may not be able to catch up with the rest of the class. To help ensure that all learners are able to work through the whole process, we provide the solution files. This includes all of the output files for each step in the data processing pipeline, as well as the scripts that the learners write collaboratively with the Instructors throughout the workshop. These files are available on the hidden .backup_dc_workshopdirectory.

Make sure to tell your helpers about the .backup_dc_workshop directory so that they can use these resources to help learners catch up during the workshop.

Notes for the Workshop

The tree of the directories whe you download the data should look like:

Notes for the Pangenome Analysis in Prokaryotes lesson

FIXME: Add 💢

Notes for the Genome Mining lesson