Welcome to chloroscan’s documentation!

Contents:

• ChloroScan: A metagenomic workflow to recover chloroplast genomes.
  • A snakemake workflow for MMA metagenomics for recovering chloroplast genomes.
  • Installation
  • Configuration database
• Command Line Interface
  • run
  • config
  • env
  • info
  • profile
  • script
  • github
  • docs
• Beginner’s tutorial
  • Data Input and configuration
• Inputs and Outputs
  • 1. Corgi predictions
  • 2. binning results
  • 3. CAT
  • 4. Summary files
  • 5. Refinement module
  • 6. cds-extraction
  • 7. Visualizations
  • 8. Some notes.
• Credits

Indices and tables

• Index

• Module Index

• Search Page