sphinx-quickstart on Tue Nov 21 15:42:50 2017. You can adapt this file completely to your liking, but it should at least contain the root toctree directive.

Welcome to DamageProfiler’s documentation!

This is the main DamageProfiler documentation, where you can find information about the prerequisites, the installation and the usage of this tool.

Contents:

• Prerequisites for the installation of DamageProfiler
  • Operating System Support
  • Software Requirements for DamageProfiler
• Installation Instructions for DamageProfiler
  • JAR file
  • Bioconda
  • Old releases
• General Usage
  • How to run
  • GUI
  • Log file
• Output Files
  • damagePlot.pdf
  • 5pCtoT_freq.txt and 3pGtoA_freq.txt
  • length_plot.pdf
  • lgdistribution.txt
  • edit_distance.pdf
  • editDistance.txt
  • misincorporation.txt
  • 5p_freq_misincorporations.txt and 3p_freq_misincorporations.txt
  • DNA_comp_genome.txt
  • DNA_composition_sample.txt
  • dmgprof.json
  • DamageProfiler.log
• Graphical User Interface
  • Load input files
  • Run configuration
  • Exploration of results
  • Metagenomic mapping file
• Runtime Estimation
  • How to run
  • How is the runtime calculated

Indices and tables

• Index
• Module Index
• Search Page