bio-assembly-qclisted

# Bio Assembly QC Assemble genomes/metagenomes and produce assembly QC artifacts. ## Instructions 1. Validate the assembly manifest and inspect a restartable execution plan before starting expensive work: ```bash uv run --no-project python skills/bio-assembly-qc/scripts/run_assembly_qc.py \ assemblies.tsv --out results/bio-assembly-qc uv run --no-project python 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`, normalizes assembler-specific outputs to per-sample `contigs.fasta`, chooses QUAST versus MetaQUAST from the declared mode, and reuses only non-empty declared outputs. 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