bio-assembly-qc

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:

   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.

2. 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.

3. 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.

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

5. 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.

6. 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.