end-reason

Oxford Nanopore read end reason QC analysis. Use when analyzing nanopore sequencing quality, checking for adaptive sampling efficiency, investigating read termination patterns, diagnosing sequencing issues, or running QC on POD5/Fast5 data. Integrates with ont-experiments for provenance tracking via Pattern B orchestration. Supports signal_positive, unblock_mux_change, data_service_unblock_mux_change analysis with quality thresholds.

End Reason Analysis - ONT QC

Analyze Oxford Nanopore read end reasons for quality assessment and adaptive sampling efficiency.

Integration

Run through ont-experiments for provenance tracking:

ont_experiments.py run end_reasons exp-abc123 --json results.json --plot qc.png

Or standalone:

python3 end_reason.py /path/to/data --json results.json

End Reason Categories

| End Reason | Description | Expected % | |------------|-------------|------------| | signal_positive | Normal completion | 80-95% | | unblock_mux_change | Adaptive sampling rejection | 0-15% | | data_service_unblock_mux_change | Basecall-triggered rejection | 0-10% | | mux_change | Pore mux change | 1-5% | | signal_negative | Signal lost | <5% |

Quality Assessment

| Status | Criteria | |--------|----------| | ✓ OK | signal_positive ≥75% | | ⚠ CHECK | signal_positive <75% or anomalies | | ✗ FAIL | signal_positive <50% |

Options

| Option | Description | |--------|-------------| | --json FILE | Output JSON summary | | --csv FILE | Output per-read CSV | | --plot FILE | Output bar chart (PNG/PDF) | | --format FORMAT | Force format (pod5, fast5, summary) | | --quick | Sample 10k reads only |

Supported Formats

POD5 (fastest, recommended)
Fast5 (legacy)
sequencing_summary.txt

Output JSON

{
  "total_reads": 15000000,
  "quality_status": "OK",
  "signal_positive_pct": 90.0,
  "unblock_mux_pct": 8.0,
  "data_service_pct": 1.0,
  "end_reasons": {
    "signal_positive": {"count": 13500000, "pct": 90.0},
    "unblock_mux_change": {"count": 1200000, "pct": 8.0}
  }
}