escpod summary¶

Generate a comprehensive summary of POD5 file(s) including read statistics, QC metrics, and run metadata.

escpod summary

Usage¶

escpod summary <INPUT> [--json]

Arguments¶

Argument	Description
`<INPUT>`	Input POD5 file or directory containing POD5 files

Options¶

Option	Description
`--json`	Output as JSON instead of formatted table
`-h, --help`	Print help

Features¶

Directory Support: Point to a directory and automatically process all *.pod5 files recursively
Read Statistics: N50, mean, median read lengths with distribution sparkline
Run Metadata: Flow cell, sequencing kit, sample ID, protocol info
QC Metrics: Active channel count, well distribution, end reason breakdown
Warnings: Alerts for old POD5 versions or corrupted files

Examples¶

Single File¶

escpod summary experiment.pod5

Directory of Files¶

escpod summary pod5_pass/

JSON Output¶

escpod summary experiment.pod5 --json

Output¶

Terminal Output¶

┌─────────────────────────────────────────────────────────────────────────────┐
│ POD5 Summary: experiment.pod5                                               │
├─────────────────────────────────────────────────────────────────────────────┤
│  1.2 GB Size │  10,543 Reads │   4 kHz Rate │  36.6 hrs Duration           │
├─────────────────────────────────────────────────────────────────────────────┤
│ Flow Cell    FAK12345 (FLO-MIN106)  │ Kit          SQK-LSK109              │
│ Sample       sample_001             │ Protocol     sequencing_MIN106_DNA   │
│ Started      2024-01-15 10:30 UTC   │ Software     MinKNOW 23.04.5         │
├─────────────────────────────────────────────────────────────────────────────┤
│ READ LENGTH (samples)                                                       │
│   N50       65,000 │ Mean    50,000 │ Median   42,000 │ Range   1K-500K    │
│   ▁▂▃▄▅▆▇█▇▆▅▄▃▂▁▁▁▁▁▁ length distribution                                │
├─────────────────────────────────────────────────────────────────────────────┤
│ CHANNELS   450/512 active (87.9%)                                           │
├─────────────────────────────────────────────────────────────────────────────┤
│ END REASONS                                                                 │
│   signal_positive          ████████████████████ 80.6%  (  8,500)            │
│   signal_negative          ███░░░░░░░░░░░░░░░░░ 14.2%  (  1,500)            │
│   mux_change               █░░░░░░░░░░░░░░░░░░░  3.8%  (    400)            │
│   unblock_mux_change       ░░░░░░░░░░░░░░░░░░░░  1.4%  (    143)            │
└─────────────────────────────────────────────────────────────────────────────┘

JSON Output¶

{
  "files": [
    {
      "path": "experiment.pod5",
      "size_bytes": 1288490188,
      "read_count": 10543,
      "batch_count": 11,
      "pod5_version": "1.0",
      "software": "MinKNOW",
      "file_identifier": "abc123-def456"
    }
  ],
  "run_info": {
    "acquisition_id": "abc123-def456",
    "acquisition_start_time": "2024-01-15 10:30 UTC",
    "sample_rate": 4000,
    "flow_cell_id": "FAK12345",
    "flow_cell_product_code": "FLO-MIN106",
    "sequencing_kit": "SQK-LSK109",
    "sample_id": "sample_001",
    "experiment_name": "my_experiment",
    "protocol_name": "sequencing_MIN106_DNA",
    "software": "MinKNOW 23.04.5",
    "system_name": "MinION",
    "system_type": "Mk1C"
  },
  "statistics": {
    "total_samples": 527150000,
    "length_min": 1000,
    "length_max": 500000,
    "length_mean": 50000.0,
    "length_median": 42000,
    "length_n50": 65000,
    "active_channels": 450,
    "total_channels": 512
  },
  "end_reasons": {
    "signal_positive": 8500,
    "signal_negative": 1500,
    "mux_change": 400,
    "unblock_mux_change": 143
  },
  "warnings": []
}

Warnings¶

The command displays warnings for:

Old POD5 versions: Files using an older POD5 format version
Corrupted files: Files that cannot be opened or read
Read errors: Individual reads that fail to parse

Example with warnings:

┌─────────────────────────────────────────────────────────────────────────────┐
│ POD5 Summary: pod5_pass/ (24 files)                                         │
├─────────────────────────────────────────────────────────────────────────────┤
...
├─────────────────────────────────────────────────────────────────────────────┤
│ ⚠ WARNINGS                                                                  │
│   2 file(s) could not be read                                               │
│   Corrupted/unreadable file: pod5_pass/bad_file.pod5 (Invalid signature)    │
│   Old POD5 version: legacy.pod5 uses v0.3 (current: 1.0)                    │
└─────────────────────────────────────────────────────────────────────────────┘

Notes¶

When processing a directory, all *.pod5 files are found recursively
Statistics are aggregated across all files
Run info is taken from the first valid file
Corrupted files are skipped with a warning, not fatal errors