Welcome to eukrhythmic’s documentation!

Contents:

• Installing eukrhythmic
  • Downloading eukrhythmic
  • Setting up a conda environment for running Snakemake
• Execution flowchart
• Running eukrhythmic
  • How to use the pipeline from the command line
  • How to use the pipeline directly through Snakemake
• Running eukrhythmic with the sample data
• Naming your samples and helping eukrhythmic find them
  • File naming
  • The metaT_sample file
  • Autogeneration of full metaT_sample file
  • Autogeneration of “FastqFileNames” column with “SampleID” column
  • Notes about manually creating metaT_sample
• Advanced: Writing a configuration file
  • Configuration file entries
• Advanced: Adding unsupported assemblers
  • Adding new assemblers
• Intermediate files and cleanup
• Common errors you may encounter
• Acknowledgments

Source Code

You can find the source for eukrhythmic on GitHub.

Indices and tables

• Index
• Module Index
• Search Page