Assess genome, transcriptome, and protein completeness with BUSCO v6 and OrthoDB lineages.
npx skills add https://github.com/ClawBio/ClawBio --skill busco-assessor
Please help me install this Agent Skill. Skill: busco-assessor Source: https://github.com/ClawBio/ClawBio/tree/main/skills/busco-assessor Command: npx skills add https://github.com/ClawBio/ClawBio --skill busco-assessor
Choosing the correct OrthoDB lineage dataset, constructing BUSCO commands, and interpreting C/S/D/F/M completeness scores requires bioinformatics expertise. This Skill automates lineage selection from a plain organism description, runs BUSCO v6, and produces an interpreted, reproducible completeness report.
Ask the agent to check the completeness of your assembly FASTA file, for example by saying "run a BUSCO assessment on my E. coli genome assembly".
High-intent search queries and answers about installing and using this skill.
Run the skill with your assembly FASTA and an organism hint, for example --input assembly.fna --organism "E. coli". It infers the correct lineage, runs BUSCO genome mode, and writes an interpreted report with C/S/D/F/M completeness scores.
Pass a free-text organism description via --organism and the skill maps it to the correct lineage using a keyword routing table or the NCBI Taxonomy API. Eukaryotes use _odb10 datasets while prokaryotes and archaea use _odb12.
Yes, the --demo flag generates a fully synthetic FASTA and BUSCO outputs in pure Python, producing a bacteria-like completeness report without any external tools. The --demo-live flag downloads a real S. cerevisiae mitochondrial genome and queries NCBI Taxonomy.
Auto-lineage requires SEPP version exactly 4.5.5; version 4.5.6 is incompatible with BUSCO auto-lineage files and silently produces wrong lineage assignments. Pin sepp=4.5.5 in your conda environment alongside busco=6.0.0.
Proteins mode requires an amino-acid FASTA (.faa); passing a nucleotide file (.fna/.fa) completes silently with zero hits. The script emits a warning when it detects this mismatch, so always use protein sequences for proteins mode.
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