bio-reads-qc-mapping
Installation
SKILL.md
Bio Reads QC Mapping
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
Instructions
- Parse sample sheet and validate inputs.
- For short reads: Run QC/trimming (bbduk).
- For long reads: Trim adapters (Porechop) and filter by quality/length (Filtlong).
- Map reads (bbmap or minimap2) and generate coverage tables.
Quick Reference
| Task | Action |
|---|---|
| Run workflow | Follow the steps in this skill and capture outputs. |
| Validate inputs | Confirm required inputs and reference data exist. |
| Review outputs | Inspect reports and QC gates before proceeding. |
| Tool docs | See docs/README.md. |
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