Agent skill · research science · aiskillstore
gget
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
Why this skill is useful
Provides specific commands and patterns for querying multiple bioinformatics databases that the AI wouldn't reliably generate on its own.
What it needs
Requires gget installed locally. About 10k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
gget Overview gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, expression data, and disease associations through a consistent interface. All gget modules work both as command-line tools and as Python functions. Important: The databases queried by gget are continuously updated, which sometimes changes their structure. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary. Installation Install gget in a clean virtual environment to avoid conflicts: Quick Start Basic usage pattern for all modules: Most modules return: Command-line: JSON (default) or CSV with -csv flag Python: DataFrame or dictionary Common flags across modules: -o/--out: Save results to file -q/--quiet: Suppress progress information -csv: Return CSV format (command-line only) Module Categories 1. Reference & Gene Information gget ref - Reference Genome Downloads Retrieve download links and metadata for Ensembl reference genomes. Parameters: species: Genusspecies format (e.g., 'homosapiens', 'musmusculus'). Shortcuts: 'human', 'mouse' -w/--which: Specify return types (gtf, cdna, dna, cds, cdrna, pep). Default: all -r/--release: Ensembl release number (default: latest) -l/--listspecies: List available vertebrate species -liv/--listivspecies: List available invertebrate species -ftp: Return only FTP links -d/--download: Download files (requires curl) Examples: gget search - Gene Search Locate genes by name or description across species. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/gget--0d07df