bio-assembly-qclisted

# 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. 3. Run QUAST v5.3+ (use MetaQUAST for metagenomes) and summarize metrics. 4. For every produced `contigs.fasta`, invoke `/tracki