scverse/gget
🧬 gget enables efficient querying of genomic reference databases
What it solves
gget simplifies the process of querying genomic databases, which often requires navigating multiple complex interfaces or writing extensive custom scripts. It provides a unified, single-line interface for fetching genomic references, annotations, sequences, and other biological data.
How it works
It is implemented as a command-line tool and Python package consisting of interoperable modules. Each module is dedicated to a specific type of database query, allowing users to perform complex tasks—such as searching for genes, retrieving amino acid sequences, and performing sequence alignments—using simple commands.
Who it’s for
Bioinformaticians, genomic researchers, and biologists who need to efficiently retrieve and analyze genomic data from various public databases.
Highlights
- Multi-database support: Query Ensembl, NCBI Virus, Protein Data Bank (PDB), and CellxGene.
- Sequence analysis: Integrated tools for BLAST, BLAT, MUSCLE, and DIAMOND alignments.
- Detailed genomic info: Retrieve gene/transcript information, amino acid sequences, and tissue expression data via ARCHS4.
- Functional analysis: Perform ontology analysis using Enrichr and find Eukaryotic Linear Motifs (ELMs).
- Cross-language support: Fully functional via CLI, Python, and R (via reticulate).
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