Home - Kinggerm/GetOrganelle GitHub Wiki

Installation

• Option 1. Use conda - one-command for GetOrganelle & all required dependencies.
• Option 2. Using the setup.py
• Option 3. In situ configuration - for developers
• Updating GetOrganelle
• Dependencies

Initialization

• Default Database Directory
• Option 1. Initialization from Github - recommended, one-command
• Option 2. Initialization using local files

Examples

• Example 1 - a one-minute testing dataset.
  • Quickstart
  • Running log
  • Output
• Example 2 - the same testing dataset with a user-defined seed.
  • Quickstart
  • Running log
  • Output
• Example 3 - Plastome (chloroplast genome) assembly using a real dataset.
• Example 4 - Animal mitogenome assembly using a real dataset.
• Example 5 - Fungal mitogenome assembly using a real dataset.

Usage

• Main scripts
  • get_organelle_from_reads.py
  • get_organelle_from_assembly.py
• Utilities
  • Utilities/slim_graph.py
  • summary_get_organelle_output.py

Q&A

• FAQ
  • General
  • Input
  • Output
• Github issues
• GoogleGroups