How do I install the Bio Reads Qc Mapping skill?

Run npx skillmds@latest add gabrielmoreira/bio-reads-qc-mapping in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Bio Reads Qc Mapping safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Bio Reads Qc Mapping?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Bio Reads Qc Mapping free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Bio Reads Qc Mapping?

gabrielmoreira (@gabrielmoreira) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bio Reads Qc Mapping by gabrielmoreira

Name: Bio Reads Qc Mapping
Rating: 4.2 (5 reviews)
Author: gabrielmoreira

File contents

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 and adapter/quality trimming with bbduk or fastp v1.3.3+.
For long reads: trim adapters with Porechop_ABI (preferred; the original Porechop is unmaintained and ships stale adapter sets) or Pychopper for full-length cDNA. Filter by quality and length with filtlong v0.2.1.
Map reads and produce coverage tables:
- Short reads, CPU: bbmap or bwa-mem2 v2.2.1+. Short reads, GPU node available: NVIDIA Parabricks fq2bam (wraps bwa-mem2 + GATK markdup; typically 3–4× faster than bwa-mem2 on 8 cores and up to ~80× over a 96-core CPU pipeline).
- Long reads, CPU: minimap2 v2.30+. AVX-512 hardware: mm2-fast as a drop-in replacement (~1.8× speedup). GPU node available: mm2-gb or mm2-ax for CUDA-accelerated long-read alignment.
Record the tool, version, and any GPU device used in the run log.

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`.

Input Requirements

Prerequisites:

Tools available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
Sample sheet and reads are available. Inputs:
sample_sheet.tsv
reads/*.fastq.gz
reference.fasta (optional)

Output

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/

Quality 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.
Validate sample sheet schema and FASTQ integrity.

Examples

Example 1: Expected input layout

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

Troubleshooting

Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.

---name: bio-reads-qc-mappingdescription: Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.--- # Bio Reads QC Mapping Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats. ## Instructions 1. Parse sample sheet and validate inputs. 2. For short reads: run QC and adapter/quality trimming with `bbduk` or `fastp` v1.3.3+. 3. For long reads: trim adapters with `Porechop_ABI` (preferred; the original `Porechop` is unmaintained and ships stale adapter sets) or `Pychopper` for full-length cDNA. Filter by quality and length with `filtlong` v0.2.1. 4. Map reads and produce coverage tables: - Short reads, CPU: `bbmap` or `bwa-mem2` v2.2.1+. Short reads, GPU node available: NVIDIA Parabricks `fq2bam` (wraps `bwa-mem2` + GATK markdup; typically 3–4× faster than `bwa-mem2` on 8 cores and up to ~80× over a 96-core CPU pipeline). - Long reads, CPU: `minimap2` v2.30+. AVX-512 hardware: `mm2-fast` as a drop-in replacement (~1.8× speedup). GPU node available: `mm2-gb` or `mm2-ax` for CUDA-accelerated long-read alignment. 5. Record the tool, version, and any GPU device used in the run log. ## 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`. | ## Input Requirements Prerequisites: - Tools available in the active environment (Pixi/conda/system). See `docs/README.md` for expected tools. - Sample sheet and reads are available. Inputs: - sample_sheet.tsv - reads/*.fastq.gz - reference.fasta (optional) ## Output - 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/ ## Quality 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. - [ ] Validate sample sheet schema and FASTQ integrity. ## Examples ### Example 1: Expected input layout ```text sample_sheet.tsv reads/*.fastq.gz reference.fasta (optional) ``` ## Troubleshooting **Issue**: Missing inputs or reference databases **Solution**: Verify paths and permissions before running the workflow. **Issue**: Low-quality results or failed QC gates **Solution**: Review reports, adjust parameters, and re-run the affected step.

Frequently asked questions

Bio Reads Qc Mapping