Registry Explorer Skill

Deep inspection of source data files to extract comprehensive metadata for ONT experiments.

Purpose

This skill explores experiment source data to extract metadata that can't be inferred from names or paths:

• BAM headers: Basecaller, model, sample info from @RG/@PG tags
• POD5 files: Run metadata, device info, protocol settings
• final_summary.txt: Chemistry, basecall model, yield statistics
• sequencing_summary.txt: Per-read statistics

Quick Start

# Explore a single experiment
/registry-explorer explore exp-abc123

# Scan all local experiments for metadata
/registry-explorer scan --local

# Extract metadata from specific file types
/registry-explorer extract exp-abc123 --bam --pod5 --summary

# Check if source files exist
/registry-explorer check exp-abc123

# List files in experiment directory
/registry-explorer ls exp-abc123

Commands

explore <exp_id> - Full Exploration

Fully explore an experiment's source data:

registry_explorer.py explore exp-abc123 [--verbose]

# Checks for and parses:
# - BAM files (header metadata)
# - POD5 files (run metadata)
# - final_summary.txt (chemistry, model, yield)
# - sequencing_summary.txt (per-read stats)
# - report_*.html (MinKNOW reports)

scan - Batch Scanning

Scan multiple experiments:

registry_explorer.py scan [--local | --public | --all]

# Options:
--missing-chemistry   Only experiments missing chemistry
--missing-model       Only experiments missing basecall_model
--limit N             Process at most N experiments
--apply               Apply changes to registry

extract - Targeted Extraction

Extract specific metadata types:

registry_explorer.py extract exp-abc123 [options]

# Options:
--bam          Extract from BAM headers
--pod5         Extract from POD5 metadata
--summary      Extract from summary files
--all          Extract from all available sources

check - File Existence Check

Verify source files exist:

registry_explorer.py check exp-abc123

# Reports:
# - Directory exists
# - BAM files found
# - POD5 files found
# - Summary files found
# - Total size

ls - List Files

List files in experiment directory:

registry_explorer.py ls exp-abc123 [--recursive]

Metadata Extracted

From BAM Headers

From POD5 Files

From final_summary.txt

From sequencing_summary.txt

Integration with Registry

Updates to registry include:

• Metadata fields populated
• Artifacts tracked (file paths)
• Provenance updated with extraction timestamp
• Audit log updated

# Full workflow
/registry-explorer scan --local --missing-chemistry --apply
/registry-scrutinize audit

File Patterns

The explorer looks for files matching:

{location}/
├── *.bam                    # Aligned/basecalled BAM
├── pod5_pass/               # POD5 files
├── final_summary*.txt       # Run summary
├── sequencing_summary*.txt  # Per-read summary
├── report_*.html            # MinKNOW reports
└── other_reports/
    └── *.json               # Additional metadata

Examples

Extract chemistry for all local experiments

/registry-explorer scan --local --missing-chemistry --apply

Deep exploration of single experiment

/registry-explorer explore exp-abc123 --verbose

Check what files exist

/registry-explorer ls exp-abc123 --recursive