bio-assembly-qc
Assemble genomes/metagenomes and produce assembly QC artifacts.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-assembly-qc --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Expected input layout
- Troubleshooting
What does the bio-assembly-qc skill do?
Assemble genomes/metagenomes and produce assembly QC artifacts.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-assembly-qc --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.