  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.

Genomics