Validation Settings¶

The validation module supports three validation levels to balance thoroughness and performance.

Validation Levels¶

Level	Parsing	Validation	Edits	Output	Speed	Use Case
strict	All data	All data	All applied	BioPython write	Slowest	Structural validation, sequence by sequence; statistics gathered
trust (default)	All data (genome) First record only (reads)	First sequence only	All applied (genome, features) None (reads)	BioPython write (genome) File copy (reads)	Fast	Trust data, adapt file coding, name and location
minimal	None	None	None	File copy	Fastest	Rename and move files to meet the requirements

Validates every record in the file
Performs comprehensive quality checks
Generates detailed statistics
Feature files: runs coordinate validation in parallel (when threads > 1 and file has ≥ 1000 features); falls back to direct parsing if gffread produces no output; fails validation if both paths return 0 features
Recommended for first-time data processing

Use when: - Processing data for the first time - Data quality is uncertain

Use when: - Data has been pre-validated - Files are from trusted sources - You need faster processing times

Use when: - Files are already in correct format - You're absolutely certain of data quality - Only file organization is needed

Set the validation level in your config.json:

{
  "ref_genome_filename": {
    "filename": "reference.fasta",
    "validation_level": "strict",
    "threads": 8
  }
}

Or set globally in options:

{
  "options": {
    "validation_level": "trust",
    "threads": 8
  }
}

Relative speed uses strict as the baseline (slowest).