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2.0.0

About CulebrONT

  • From assembly to correction
    • Assembly
    • Optional circularisation
    • Polishing
    • Correction
  • Quality on assemblies

Install

  • Requirements
  • Install culebrONT PyPI package
  • Steps for LOCAL installation
    • culebrONT install_local
  • Steps for HPC installation
    • culebrONT install_cluster
    • 1. Adapt profile and cluster_config.yaml
    • 2. Adapt tools_path.yaml
  • Check install
    • culebrONT test_install
  • Advance installation
    • 1. Snakemake profiles
      • Preparing the profile’s config.yaml file
    • 2. Adapting cluster_config.yaml
    • 3. How to configure tools_path.yaml
    • And more …
      • How to build singularity images
      • Threading rules inside culebrONT

Defining Workflows

  • How to create a workflow
    • culebrONT create_config
    • 1. Providing data
    • 2. Choose assemblers, polisher and correctors
    • 3. Choose quality tools
    • 4. Parameters for some specific tools
  • How to run the workflow
    • culebrONT run_cluster
    • culebrONT run_local
  • Advance run
    • Provide more ressources
      • culebrONT edit_cluster_config
    • Provide own tools_config.yaml
      • culebrONT edit_tools
  • Output on CulebrONT
  • Report

Project Info

  • Citation
    • Useful notes
    • Thanks
  • License

FAQ

  • Frequently Asked Questions

API

  • culebrONT
    • create_config
    • edit_cluster_config
    • edit_tools
    • install_cluster
    • install_local
    • run_cluster
    • run_local
    • test_install
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© Copyright 2019-2022, J Orjuela (IRD), A Comte (IRD), S Ravel (CIRAD), F Charriat (INRAE), T Vi (IRD, AGI), F Sabot (IRD) and S Cunnac (IRD) Revision 45a86e6d.