Comparative evaluation of bacterial pan-genome analysis tools

Master's Thesis of Benjamin Otter

This repository contains a collection of scripts I used for data generation and data analysis during my Master's Thesis. It is organized in 4 subfolders:

data generation

• nextflow .nf scripts for data generation
• conda environment .yml files

benchmark

• nextflow .nf scripts to run each tool
• format scripts for each tool
• conda environment .yml files

results analysis

• formatted output files .json of all runs
• IPython notebooks .ipynb used to generate plots for each bacterial species
• additional analysis scripts .py

results benchmark

• raw benchmark data .txt trace files
• IPython notebooks .ipynb used to compute and plot benchmark results
• additional scripts