genomepy: genes and genomes at your fingertips

Area of Science:

• Genomics
• Bioinformatics

Background:

• Functional genomics experiments (ATAC-, ChIP-, RNA-sequencing) rely on accurate genomic resources like reference genome assemblies and gene annotations.
• Manually retrieving and managing these resources from various sources and versions is often tedious and error-prone for bioinformatic workflows.

Purpose of the Study:

• To present genomepy, a tool designed to automate the acquisition and preprocessing of genomic data for functional genomics analyses.
• To streamline the process of obtaining and preparing necessary genomic resources, reducing manual effort and potential errors.

Main Methods:

• Genomepy searches and downloads genomic data from major repositories including NCBI, Ensembl, UCSC, and GENCODE.
• The tool inspects available gene annotations to facilitate informed selection and offers automated preprocessing with controllable defaults.
• Genomepy can also generate or download supplementary data such as aligner indexes, genome metadata, and blacklists.

Main Results:

• Genomepy successfully automates the search, download, and preprocessing of genomic data, including reference genomes and gene annotations.
• The tool supports multiple data sources and provides options for automated generation or download of essential supporting data.
• Users can make informed decisions regarding genomic data selection through annotation inspection.

Conclusions:

• Genomepy significantly simplifies and standardizes the process of obtaining and preparing genomic resources for functional genomics studies.
• The tool enhances reproducibility and efficiency in bioinformatics by automating a critical, often manual, step.