genome-annotation

Plugin genome-annotation from marketplace musser-lab in MusserLab/lab-claude-skills. Commands read from the repo's manifest — 19 days ago.

Skills (5)

• busco

  Run BUSCO completeness assessment on genomes, transcriptomes, or predicted proteomes. Generates conda env setup, shared-lineage download, SLURM array scripts with sample-sheet-driven (input × lineage) fan-out, a local single-input fallback, and an aggregator. Use when running BUSCO, assessing genome

• gene-lookup

  Look up gene or protein information from biological database IDs and accessions. Use when working with gene IDs, protein accessions, or identifiers from UniProt, Ensembl, FlyBase, WormBase, NCBI/RefSeq, or similar databases. Covers: identifying what database an ID comes from, converting IDs to gene

• hmmer

  Run HMMER profile-HMM searches (hmmscan / hmmsearch / phmmer / hmmbuild / jackhmmer) for protein-family detection, marker-gene extraction from assemblies, and custom HMM profiles. Generates conda env setup, Pfam-HMM download + hmmpress, SLURM array scripts with sample-sheet fan-out, a local single-i

• protein-phylogeny

  Protein (gene) phylogeny inference pipeline: generates a .qmd analysis script that performs alignment, optional trimming, and tree building. Use when building phylogenetic trees from protein sequences, aligning protein families, running IQ-TREE or MAFFT for phylogenetics, or when the user says "gene

• tree-formatting

  Phylogenetic tree visualization and formatting with ggtree (R) or iTOL (web). Use when rendering a phylogenetic tree as a figure, choosing tree layout, coloring branches or labels by taxonomy, collapsing clades, displaying support values, or adding overlays to a tree. Do NOT load for tree inference

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