Welcome to EUKulele’s documentation!

Contents

• EUKulele Quick Start
  • Installation
  • Generalized flow of EUKulele annotation
  • Metagenome-assembled genome (MAG) annotation
  • Metatranscriptomic (MET) annotation
• About EUKulele
  • Functionality
  • Usage and Dependencies
• Using EUKulele
  • Metatranscriptomes (METs)
  • Metagenome Assembled Genomes (MAGs)
  • LCA Algorithm
• Installation
  • Installing with conda
  • Installing with mamba
  • Installing with Pip
  • Cloning the Development Code from GitHub
• Invocation
  • Less common use cases
• Installing Databases and Creating Configuration Files
  • Default Databases
  • Composition of Default Databases
  • Recommendations for Database Usage
  • Using Other Databases
  • Customizing the Taxonomic Identification Cutoffs
• Expected Output of EUKulele
  • Taxonomy Estimation Folders
  • Taxonomy Counts Folders
  • Taxonomy Visualization Folders
• Trying out EUKulele
• Community Guidelines
  • How to contribute to EUKulele
  • Submitting an issue / Asking for help
  • Collaborations

Documentation

• API
• Parameters
• Auxiliary Scripts
  • Create Protein Table
  • Download Database

Source Code

You can find the source for EUKulele on GitHub.

Badging

Flowchart

Caveats

See Using EUKulele for caveats about the use of predicted proteins, rather than nucleotide contigs, for metagenomic sequences.

Indices and tables

• Index
• Module Index
• Search Page