Welcome to KmerWorkflow’s documentation!

Today, get an assembly of large polyploid genome is very complicated and it’s hard to compare lot of individuals of this polyploid species, in particular to compare sequences of many individuals.

Due to the daily deluge of data sequences the number of data increase and need to be analyse …

KMER_WORKFLOW is is an open-source, scalable, modulable and traceable snakemake pipeline, able to compare multiple data short read (NGS) obtained from illumina sequencing by counting the number of shared kmers. The workflow KMER_WORKFLOW can help you to find which individuals share sequences informations to other.

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
  • 2. Adapting cluster_config.yaml
  • 3. How to configure tools_path.yaml

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
  • Providing your own tools_config.yaml
• Output on Kmerworkflow

Project Info

• Citation
• License

API

• Kmerworkflow
  • create_config
  • edit_cluster_config
  • edit_tools
  • install_cluster
  • install_local
  • run_cluster
  • run_local
  • test_install

Indices and tables

• Index

• Module Index

• Search Page