genomepy: genes and genomes at your fingertips

TL;DR

Genomepy simplifies the process of retrieving, comparing, and preprocessing genomic data and annotations from multiple sources, streamlining functional genomics workflows.

Contribution

It introduces a tool that automates searching, downloading, and preprocessing genomic data from major databases with user-friendly defaults.

Findings

Supports multiple data sources including NCBI, Ensembl, UCSC, GENCODE

Enables comparison of gene annotations for informed selection

Automates generation of supporting data like aligner indexes

Abstract

Analyzing a functional genomics experiment, such as ATAC-, ChIP- or RNA-sequencing, requires reference data including a genome assembly and gene annotation. These resources can generally be retrieved from different organizations and in different versions. Most bioinformatic workflows require the user to supply this genomic data manually, which can be a tedious and error-prone process. Here we present genomepy, which can search, download, and preprocess the right genomic data for your analysis. Genomepy can search genomic data on NCBI, Ensembl, UCSC and GENCODE, and compare available gene annotations to enable an informed decision. The selected genome and gene annotation can be downloaded and preprocessed with sensible, yet controllable, defaults. Additional supporting data can be automatically generated or downloaded, such as aligner indexes, genome metadata and blacklists. Genomepy is freely available at https://github.com/vanheeringen-lab/genomepy under the MIT license and can be installed through pip or bioconda.