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About KmerWorkflow

  • Sub_Sampling reads Illumina and count KMERS
  • Calculate intersection of KMERS between individuals
  • UPSET PLOT , KMER intersection graph

Install

  • Requirements
  • Install Kmerworkflow PyPI package
  • Steps for LOCAL installation
    • install_local
  • Steps for HPC distributed cluster installation
    • install_cluster
    • 1. Adapt profile and cluster_config.yaml
    • 2. Adapt tools_path.yaml
  • Check install
    • 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
      • Threading rules inside Kmerworkflow

Defining Workflows

  • How to create a workflow
    • create_config
    • 1. Providing data
    • 2. Parameters for some specific tools
    • 3. Parameters for some specific tools and give name of output
  • How to run the workflow
    • run_cluster
    • run_local
  • Advance run
    • Providing more resources
      • edit_cluster_config
    • Providing your own tools_config.yaml
      • edit_tools
  • Output on Kmerworkflow

Project Info

  • Citation
    • Thanks
  • License

API

  • Kmerworkflow
    • create_config
    • edit_cluster_config
    • edit_tools
    • install_cluster
    • install_local
    • run_cluster
    • run_local
    • test_install
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© Copyright 2023-2023, T Durand (CIRAD). Revision c6e8c952.