Bio Assembly QC

Assemble isolate genomes or metagenomes from QC-passed reads, normalize the assembler output to one contigs.fasta per sample, and run QUAST or MetaQUAST.

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 --threads 4
   # Inspect run_manifest.json, then execute the same plan on a compute node:
   uv run --script skills/bio-assembly-qc/scripts/run_assembly_qc.py \
     assemblies.tsv --out results/bio-assembly-qc --threads 16 --execute