This repository contains scripts for evaluating SECEDO, available at: https://github.com/ratschlab/secedo

This repository also contains all the information needed to reproduce the experimental results in the associated SECEDO paper.

Please follow the installation instructions in the SECEDO repository before running the experiments.

Directories:

• breast_cancer: download instructions and scripts for preprocessing the Breast Cancer 10xGenomics data, for creating pileup files and for running SECEDO on it
• varsim: scripts for generating and running experiments on synthetic data

All scripts are written in basic bash and are using LSF to launch jobs. The scripts are readable and well-documented, and should be easy to adapt for your needs.