Genomepy: genes and genomes at your fingertips.

ABSTRACT:

Motivation

Analyzing a functional genomics experiment, such as ATAC-, ChIP-, or RNA-sequencing, requires genomic resources such as a reference genome assembly and gene annotation. These data 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.

Results

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 inspect available gene annotations to enable an informed decision. The selected genome and gene annotation can be downloaded and preprocessed with sensible, yet controllable, defaults.

SUBMITTER: Frolich S 

PROVIDER: S-EPMC10017095 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature