This GitHub is primarily to document the scripts I have used for this project. I hope future students will find it helpful, but it is by no means written with the intention of being easy to understand. Anyone who is also working on this project should find this helpful, but you will need to read through the scripts and make sure you understand what it's doing.
run_all: This takes a directory full of forward and reverse reads, sorts them into individual folders (one per sample), and runs the assembly/annotation pipeline for each folder
cat_samples: This is a simple script used to concatenate the L001 and L002 samples of each isolate type
The scripts should be somewhat annotated, so read through the comments within the scripts for help.
(Note: This repo is a submodule for the entire project. Anything in this repo is in scripts/ of the main project repo)