scverse/gget

Health v2 · maintenance only

Adoption not part of the score

1195 stars · 93 forks observed · 2026-09-01

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

gget is a free, open-source Python package and command-line tool for efficiently querying genomic reference databases such as Ensembl, UniProt, NCBI, and AlphaFold. It consists of interoperable modules that each perform a type of database query (gene search, sequence retrieval, BLAST, enrichment analysis, ortholog lookup) in a single line of code.

Use cases

• fetch Ensembl reference and annotation files for a species
• search for genes by name or description and get their Ensembl IDs
• retrieve gene and transcript metadata from an Ensembl ID
• fetch amino acid or nucleotide sequences of genes
• BLAST or align a sequence against reference databases
• run enrichment analysis on a list of genes
• find orthologs of a gene across species
• query protein structure predictions from AlphaFold

When to choose

• you need quick programmatic or command-line access to genomic reference databases like Ensembl, UniProt, or NCBI
• you want one-line queries for gene info, sequences, or orthologs in Python or Jupyter
• you need sequence alignment (BLAST/BLAT/diamond/muscle) without setting up local databases
• you are doing transcriptomics or proteomics work and want enrichment analysis or AlphaFold structure lookups

When to avoid

• you need a full-featured genome browser or heavy-duty local bioinformatics pipelines
• you require offline access to genomic databases with no internet queries
• you need a graphical interface rather than CLI or Python API
• your work is outside genomics/proteomics and unrelated to biological reference data

Facets

library · maturity active

search-engine cli sdk data-science bioinformatics data-science developer-tools python cli cross-platform genomics ensembl uniprot alphafold blast enrichment-analysis bioinformatics transcriptomics proteomics single-cell

Member repositories

For agents

markdown · JSON · MCP: product_card(name="scverse/gget")