Welcome to coproID’s documentation!

Contents:

• Introduction
  • A fully reproducible pipeline for COPROlite and paleofeces host IDentification
  • Quick Start
  • Documentation
  • Credits
  • Contributions and Support
  • Citing
  • Contributors
  • Tool references
• 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
  • coproID_report.html
  • coproID_result.csv
  • coproID_bp.csv
  • kraken
  • damageprofiler
  • alignments
  • pmdtools
  • pipeline_info

Indices and tables

• Index
• Module Index
• Search Page