# Bio Assembly Qc > Assemble genomes/metagenomes and produce assembly QC artifacts. - **Type:** Skill - **Install:** `agentstack add skill-fmschulz-omics-skills-bio-assembly-qc` - **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior - **Seller:** [fmschulz](https://agentstack.voostack.com/s/fmschulz) - **Installs:** 0 - **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills) - **Latest version:** 0.1.0 - **License:** MIT - **Upstream author:** [fmschulz](https://github.com/fmschulz) - **Source:** https://github.com/fmschulz/omics-skills/tree/main/skills/bio-assembly-qc - **Website:** https://fmschulz.github.io/omics-skills/ ## Install ```sh agentstack add skill-fmschulz-omics-skills-bio-assembly-qc ``` Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent. ## About # 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 bacterial isolates (PacBio CLR, ONT): Flye v2.9.5+ for the draft/baseline assembly. Use Autocycler v0.6+ when a complete, high-confidence bacterial consensus genome is needed from multiple independent long-read assembly attempts; do not use it for mixed-community metagenomes. - Long-read metagenomes: Flye v2.9.5+ in `--meta` mode (metaFlye) as the baseline for ONT/CLR mixed-community assemblies. - 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. - For very large ONT/metagenome FASTQs, use `/bio-reads-qc-mapping` guidance for filtering and avoid redundant full-file raw-read preflights before filtering. Record raw file metadata (`stat` path, size, mtime), optionally run a small sampled check, and write `seqkit stats` after each produced read set. - Use atomic output patterns for long-running filters and assemblies: write to `.tmp`, verify non-empty/readable output, then `mv` into the final path. Resume mode should skip existing final outputs only after sanity checks; when checks fail, use a tool-supported overwrite option or remove the corrupt final output before rerunning. - For Flye/metaFlye failures or interrupted jobs, prefer `--resume` or `--resume-from` in the existing output directory when the prior run is structurally intact. Do not delete a large partial assembly unless logs or missing stage files show it is corrupted. 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 or reads/*.fastq (raw or filtered reads; verify actual compression by content when suffixes are suspect). - assembler choice (spades | flye | metaflye | metamdbg | myloasm | autocycler). ## 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 readable. If `gzip -t` fails on a `.gz`-named file, inspect magic bytes or file type before labeling it corrupt; it may be plain FASTQ with the wrong suffix. - [ ] Check available disk space before assembly. - [ ] For large ONT/metagenome inputs, raw file metadata and post-filter `seqkit stats` are recorded without redundant full-file raw preflight scans. - [ ] Long-running filter outputs use `.tmp` plus atomic rename, and resume guards distinguish valid completed outputs from partial/corrupt files. - [ ] Flye/metaFlye logs are inspected before deciding whether to resume, rerun, or clean a partial output directory. - [ ] For Autocycler isolate consensus, record each input assembler/run and confirm the sample is not a mixed community. - [ ] 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. **Issue**: Large ONT assembly workflow appears stalled before assembly **Solution**: Check whether the script is doing a raw full-file preflight (`gzip -t`, raw `seqkit stats`) instead of productive filtering. For urgent routing/assembly, replace raw full scans with metadata plus sampled checks, then run filtering and post-filter stats. **Issue**: Flye job timed out or was interrupted **Solution**: Inspect `flye.log` and stage files. If the output directory is intact, resubmit with Flye resume options rather than restarting from scratch. ## Source & license This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code. - **Author:** [fmschulz](https://github.com/fmschulz) - **Source:** [fmschulz/omics-skills](https://github.com/fmschulz/omics-skills) - **License:** MIT - **Homepage:** https://fmschulz.github.io/omics-skills/ Install and usage instructions live in the source repository linked above. ## Pricing - **Free** — Free ## Security capabilities Automated source analysis of v0.1.0 — what this tool can access: - **Network access:** no - **Filesystem access:** no - **Shell / process execution:** no - **Environment & secrets:** no - **Dynamic code execution:** no *"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.* ## Versions - **0.1.0** — security scan: passed — Imported from the upstream source. ## Links - Listing page: https://agentstack.voostack.com/l/skill-fmschulz-omics-skills-bio-assembly-qc - Seller: https://agentstack.voostack.com/s/fmschulz - Browse the marketplace: https://agentstack.voostack.com/browse --- Listed on AgentStack — the marketplace for AI agent skills and MCP servers. 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