This repository provides all code used to describe eccDNAs in Magnaporthe oryzae.
The repository is organized by section of the manuscript.
Generally, each section contains:
- SLURM (.slurm) scripts that were used to first do the raw data processing on Berkeley's Savio computing cluster
- bash (.sh) and Python (.py) scripts that are called within the SLURM scripts to be used for data processing
- R (.Rmd) and iPython (.ipynb) notebooks used for final processing, statistical analyses and plotting.
The update_git.sh script as well as the two submodules are simply used by me to update and organize this github repository, please ignore them.
For acknowledgments, citations, and software versions, please refer to the manuscript:
The manuscript has now been published here: The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors
All analysis in this manuscript starts with outputs from the ecc_caller pipeline written for this manuscript. The version of this pipeline used for the manuscript is included in this repository.
A maintained version with detailed instructions for usage is posted in this separate repository: https://github.com/pierrj/ecc_caller
Code is freely available under the MIT license
Please feel free to contact me directly with any questions, if you have any issues with the code or if you find any script that is missing.
Pierre Joubert - @pmjoubert - pierrj@berkeley.edu
Project Link: https://github.com/pierrj/moryzae_eccdnas_manuscript_code_final