Welcome to coproID’s documentation!

Contents:

• Introduction
  • Quick start
  • coproID example workFlow
  • How to cite coproID
• Installation
• Configuration
  • Pipeline configuration
• Usage
  • Introduction
  • Running the pipeline
  • Main arguments
  • Reference genomes
  • Settings
  • Other coproID parameters
  • Job resources
  • AWS Batch specific parameters
  • Other command line parameters
• Output
  • multiqc_report.html
  • coproID_report.html
  • coproID_result.csv
  • kraken
  • damageprofiler
  • alignments
  • pmdtools

Indices and tables

• Index
• Module Index
• Search Page