# Bio Reads Qc Mapping

> Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

- Skill: `majiayu000/bio-reads-qc-mapping` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds add majiayu000/bio-reads-qc-mapping`
- Raw SKILL.md: https://api.skillmd.com/api/skills/majiayu000/bio-reads-qc-mapping/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: majiayu000 (https://skillmd.com/u/majiayu000)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/majiayu000/bio-reads-qc-mapping

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# Bio Reads QC Mapping

## When to use
- Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

## Prerequisites
- Tools installed via pixi (see pixi.toml).
- Sample sheet and reads are available.

## Inputs
- sample_sheet.tsv
- reads/*.fastq.gz
- reference.fasta (optional)

## Outputs
- results/bio-reads-qc-mapping/trimmed_reads/
- results/bio-reads-qc-mapping/qc_reports/
- results/bio-reads-qc-mapping/mapping_stats.tsv
- results/bio-reads-qc-mapping/coverage.tsv
- results/bio-reads-qc-mapping/logs/

## Steps
1. Parse sample sheet and validate inputs.
2. For short reads: Run QC/trimming (bbduk).
3. For long reads: Trim adapters (Porechop) and filter by quality/length (Filtlong).
4. Map reads (bbmap or minimap2) and generate coverage tables.

## QC gates
- Post-QC read count sanity checks pass.
- Mapping rate meets project thresholds.
- On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.

## Validation
- Validate sample sheet schema and FASTQ integrity.

## Tools
- bbtools (bbduk, bbmap) v39.52
- minimap2 v2.30
- Filtlong (long read quality filtering)
- Porechop (Nanopore adapter trimming)

## Paper summaries (2023-2025)
- summaries/ (include example use cases and tool settings used)

## Tool documentation
- [BBDuk](docs/bbduk.html) - Quality trimming and adapter removal for short reads
- [BBMap](docs/bbmap.html) - Short read aligner and coverage calculator
- [Minimap2](docs/minimap2.html) - Long read aligner
- [Filtlong](docs/filtlong.html) - Long read quality filtering
- [Porechop](docs/porechop.html) - Nanopore adapter trimming

## References
- See ../bio-skills-references.md