Individual skill
tooluniverse-microbial-genome-characterization
Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organism name or taxid to assemblies, picks the reference/representative or best-quality assembly, pulls assembly QC metrics (total length, contig/scaffold N50, contig count, GC%, assembly level, RefSeq category), enumerates chromosomes and plasmids via per-replicon sequence reports, and compares candidate assemblies on quality. Use for "what genomes are available for [organism]", "assembly stats / N50 / GC content for [GCF_/GCA_ accession]", "how many plasmids does [strain] have", "compare assemblies for [species]", "find the reference genome for [taxon]", "is this assembly Complete Genome or just contigs". NOT for gene-level orthology/synteny (use tooluniverse-comparative-genomics), plant gene structure (use tooluniverse-plant-genomics), de novo assembly from raw reads (no tool exists), or taxonomy-only name/lineage lookups.
plugins/tooluniverse/skills/tooluniverse-microbial-genome-characterization/SKILL.md
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# Microbial Genome Assembly Characterization & QC
Discover, quality-control, and structurally map genome ASSEMBLIES for any organism using the keyless NCBI Datasets genome tools. Organism/taxon in → assembly inventory, QC metrics, and chromosome/plasmid map out.
## LOOK UP, DON'T GUESS
When uncertain about an accession, assembly level, replicon count, or N50, CALL the tool. Never report assembly statistics from memory — accessions and metrics change with each RefSeq release. A live NCBI Datasets answer is always more reliable than a guess.
## COMPUTE, DON'T DESCRIBE
When comparing multiple assemblies or ranking by quality, retrieve each via the tools, then write and run Python (pandas) over the returned JSON to sort, score, and tabulate. Don't describe what you would compute — execute it and report actual numbers.
## When to Use This Skill
**Triggers**:
- "What genomes are available for [organism]?" / "Find the reference genome for [taxon]"