How do I install the Bio Assembly Qc skill?

Run npx skillmds@latest add gabrielmoreira/bio-assembly-qc 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.

What does the Bio Assembly Qc skill do?

Assemble genomes/metagenomes and produce assembly QC artifacts. It is listed under AI & ML on SkillMD.

Is Bio Assembly Qc 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 Assembly Qc?

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 Assembly Qc free to use?

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

Who published Bio Assembly Qc?

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

Bio Assembly Qc by gabrielmoreira — Agent Skill

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

File contents

Bio Assembly QC

Assemble genomes/metagenomes and produce assembly QC artifacts.

Instructions

Select an assembler based on read type, genome/metagenome scope, and sample diversity:
- Illumina short-read isolates and hybrid assemblies: SPAdes v4.0.0+ (final feature release; bug-fix-only series continues). Use metaSPAdes for short-read metagenomes.
- Long-read isolates (PacBio CLR, ONT): Flye v2.9.5+.
- Long-read metagenomes: Flye v2.9.5+ in --meta mode (metaFlye) as the baseline.
- HiFi metagenomes: prefer metaMDBG v1.1 (~2× more circularized high-quality MAGs vs metaFlye on HiFi, better virus/plasmid recovery; Nature Biotechnology 2024, DOI: 10.1038/s41587-023-01983-6). Keep metaFlye as a comparator when a per-sample failure mode is suspected.
- Diverse or very large long-read datasets where speed dominates: myloasm (2025) as a faster long-read metagenome assembler when its profile matches the dataset; document the choice in the run log.
Run assembly with resource-aware settings and record exact CLI, version, thread count, and RAM ceiling.
Run QUAST v5.3+ (use MetaQUAST for metagenomes) and summarize metrics.
For every produced contigs.fasta, invoke /tracking-taxonomy-updates to run the BBTools-container QuickClade percontig domain screen before choosing downstream genome/MAG/viral/eukaryotic workflows.
Use the QuickClade domain routing table to decide the next step:
- Bacteria/Archaea -> /bio-gene-calling, /bio-annotation, and GTDB-Tk taxonomy assignment.
- Viral or virus-like -> /bio-viromics before prokaryotic MAG tooling.
- Eukaryota -> eukaryote-aware gene/QC workflows and EukCC where bins or genomes are present.
- Mixed/low-confidence -> split or flag contigs before domain-specific analysis.

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.
Sufficient disk and RAM for chosen assembler. Inputs:
reads/*.fastq.gz (raw reads).
assembler choice (spades | flye | metamdbg | myloasm).

Output

results/bio-assembly-qc/contigs.fasta
results/bio-assembly-qc/assembly_metrics.tsv
results/bio-assembly-qc/domain_routing.tsv
results/bio-assembly-qc/qc_report.html
results/bio-assembly-qc/logs/

Quality Gates

Assembly size range and N50 distribution meet project thresholds.
On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
Verify reads are present and gzip-readable.
Check available disk space before assembly.
QuickClade percontig domain screen completed or the reason for skipping it is explicitly recorded.
Domain routing table is reviewed before selecting MAG, viral, bacterial/archaeal, or eukaryotic downstream tools.

Examples

Example 1: Expected input layout

reads/*.fastq.gz (raw reads).
assembler choice (spades | flye).

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-assembly-qcdescription: Assemble genomes/metagenomes and produce assembly QC artifacts.--- # Bio Assembly QC Assemble genomes/metagenomes and produce assembly QC artifacts. ## Instructions 1. Select an assembler based on read type, genome/metagenome scope, and sample diversity: - Illumina short-read isolates and hybrid assemblies: SPAdes v4.0.0+ (final feature release; bug-fix-only series continues). Use `metaSPAdes` for short-read metagenomes. - Long-read isolates (PacBio CLR, ONT): Flye v2.9.5+. - Long-read metagenomes: Flye v2.9.5+ in `--meta` mode (metaFlye) as the baseline. - HiFi metagenomes: prefer **metaMDBG v1.1** (~2× more circularized high-quality MAGs vs metaFlye on HiFi, better virus/plasmid recovery; *Nature Biotechnology* 2024, DOI: 10.1038/s41587-023-01983-6). Keep metaFlye as a comparator when a per-sample failure mode is suspected. - Diverse or very large long-read datasets where speed dominates: **myloasm** (2025) as a faster long-read metagenome assembler when its profile matches the dataset; document the choice in the run log. 2. Run assembly with resource-aware settings and record exact CLI, version, thread count, and RAM ceiling. 3. Run QUAST v5.3+ (use MetaQUAST for metagenomes) and summarize metrics. 4. For every produced `contigs.fasta`, invoke `/tracking-taxonomy-updates` to run the BBTools-container QuickClade `percontig` domain screen before choosing downstream genome/MAG/viral/eukaryotic workflows. 5. Use the QuickClade domain routing table to decide the next step: - Bacteria/Archaea -> `/bio-gene-calling`, `/bio-annotation`, and GTDB-Tk taxonomy assignment. - Viral or virus-like -> `/bio-viromics` before prokaryotic MAG tooling. - Eukaryota -> eukaryote-aware gene/QC workflows and EukCC where bins or genomes are present. - Mixed/low-confidence -> split or flag contigs before domain-specific analysis. ## 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. - Sufficient disk and RAM for chosen assembler. Inputs: - reads/*.fastq.gz (raw reads). - assembler choice (spades | flye | metamdbg | myloasm). ## Output - results/bio-assembly-qc/contigs.fasta - results/bio-assembly-qc/assembly_metrics.tsv - results/bio-assembly-qc/domain_routing.tsv - results/bio-assembly-qc/qc_report.html - results/bio-assembly-qc/logs/ ## Quality Gates - [ ] Assembly size range and N50 distribution meet project thresholds. - [ ] On failure: retry with alternative parameters; if still failing, record in report and exit non-zero. - [ ] Verify reads are present and gzip-readable. - [ ] Check available disk space before assembly. - [ ] QuickClade `percontig` domain screen completed or the reason for skipping it is explicitly recorded. - [ ] Domain routing table is reviewed before selecting MAG, viral, bacterial/archaeal, or eukaryotic downstream tools. ## Examples ### Example 1: Expected input layout ```text reads/*.fastq.gz (raw reads). assembler choice (spades | flye). ``` ## 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 Assembly Qc