EEfinder
  • Installation
    • Requirements
    • Install from Bioconda
    • Run with a container
      • Docker
      • Singularity / Apptainer
    • Install from PyPI
    • Install from source
    • Verify the installation
    • Next steps
  • Acquiring databases
    • The databases define the search space
    • The metadata CSV format
    • Viral database and metadata
      • Protein database (-db)
      • Protein table (-mt)
    • Bacterial database and metadata
      • Email and API key
    • Host-gene baits (-bt)
    • Indexing
  • Running EEfinder
    • Example run (with the bundled test_files/)
    • Running with DIAMOND
      • The sensitivity trade-off
    • Pipeline steps
    • Options reference
      • Required inputs
      • Search & filtering
      • Element assembly
      • Masking & output
  • Custom arguments
    • Keeping temporary files
    • Merging fragmented elements
      • Merge length (-lm / --limit)
      • Merge level (-ml / --merge_level)
    • Range junction (-rj / --range_junction)
    • Minimum contig length (-ln / --length)
    • Flank length (-fl / --flank)
    • Masking (-cm / --clean_masked and -mp / --mask_per)
    • Output prefix (-pr / --prefix)
  • Outputs
    • Main outputs
    • The taxonomy table (PREFIX.EEs.tax.tsv)
    • The cleaned outputs (--clean_masked)
    • The run log (eefinder.log)
    • Intermediate files (tmp_files/)
  • Accessory scripts
    • Preparing inputs
      • bac_retriever.py
      • ictv_ncbi.py
    • Post-processing elements
      • get_copies.py
      • get_nr_orfs.py
      • CIAling_auto.py
      • all_tax_to_tsv.py
    • Plotting
  • Developer guide
    • Package layout
    • Conventions & gotchas
    • Style
    • Build metadata
      • Dependency bounds
    • Releasing to PyPI
    • The Bioconda package
    • Building the docs locally
    • Read the Docs
EEfinder
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