ProPhyle documentation contents

• 1. Quick example
• 2. Requirements
• 3. Installing ProPhyle
  • 3.1. Installing ProPhyle using Bioconda
  • 3.2. Installing ProPhyle using PIP
  • 3.3. Running ProPhyle directly from the repository
• 4. Building a standard database
  • 4.1. Downloading genomes
  • 4.2. Index construction
• 5. Building a custom database
  • 5.1. Building a custom database with user-provided data
  • 5.2. Building a custom database with RefSeq genomes and the NCBI taxonomy
• 6. Classifying reads
• 7. Compressing indexes for transmission
  • 7.1. Compression
  • 7.2. Decompression
• 8. File formats
  • 8.1. Input data formats
  • 8.2. Assignments
  • 8.3. Abundances estimates (experimental)
  • 8.4. Internal ProPhyle formats
• 9. Command-line interface
  • 9.1. ProPhyle – the main program
  • 9.2. prophyle_assembler
  • 9.3. prophyle_index
  • 9.4. prophyle_assignment
  • 9.5. prophyle_propagation_makefile.py
  • 9.6. prophyle_propagation_preprocessing.py
  • 9.7. prophyle_propagation_postprocessing.py
  • 9.8. prophyle_validate_tree.py