end-reason

Oxford Nanopore读取结束原因的质量控制分析。用于分析纳米孔测序质量、检查自适应采样效率、研究读取终止模式、诊断测序问题或对POD5/Fast5数据进行质量控制。通过Pattern B编排与ont-experiments集成，以进行来源跟踪。支持带有质量阈值的signal_positive、unblock_mux_change、data_service_unblock_mux_change分析。

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}
  }
}