version: "1.0.1" name: bio-assembly-qc description: Assemble genomes or metagenomes and assess assembly quality. Use when turning sequence reads into contigs and reporting completeness, continuity, and contamination evidence.

Bio Assembly QC

Assemble genomes/metagenomes and produce assembly QC artifacts.

Instructions

Tool guides and versions: docs/README.md.

1. Validate the assembly manifest and inspect a restartable execution plan before starting expensive work:

``bash uv run --script skills/bio-assembly-qc/scripts/run_assembly_qc.py \ assemblies.tsv --out results/bio-assembly-qc uv run --script skills/bio-assembly-qc/scripts/run_assembly_qc.py \ assemblies.tsv --out results/bio-assembly-qc --execute ``

The driver rejects samples whose upstream read_qc_status is not passed. It normalizes assembler outputs to per-sample contigs.fasta and chooses QUAST or MetaQUAST from the declared mode. It reuses a stage only when its declared outputs are non-empty and its .done marker exists.

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.

1. 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.

1. Run QUAST v5.3+ (use MetaQUAST for metagenomes) and summarize metrics.
2. 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.
3. 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.

Input Requirements

Prerequisites:

• Tools declared in the project's pinned Pixi environment. 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).
• assemblies.tsv with sample_id, mode, read1, read2, read_qc_status, and read_platform; supported core modes are short_isolate, long_isolate, short_metagenome, long_metagenome, and hifi_metagenome. read_platform is required for long_isolate and long_metagenome, and selects the Flye error model: ont gives --nano-hq, pacbio-clr gives --pacbio-raw, pacbio-hifi gives --pacbio-hifi. Leave it empty for short-read modes; hifi_metagenome accepts only pacbio-hifi or an empty value.

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/
• stdout: the last line is one JSON envelope {ok, skill, out, manifest, warnings} (driver stdout contract in AGENTS.md)

Quality Gates

• [ ] Assembly size range and N50 distribution meet project thresholds.
• [ ] Every assembler output is normalized to a non-empty per-sample contigs.fasta before QC or downstream routing.
• [ ] On execution failure, preserve logs and report the failed command; retry only after diagnosing the cause and recording the changed parameters. Report unmet biological thresholds as results; never tune parameters solely to pass a gate.
• [ ] 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 require a stage .done marker before reusing non-empty outputs.
• [ ] 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

Use fixtures/assemblies.tsv as the executable short-read, long-read, and metagenome planning fixture.

Troubleshooting

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.