A reference genome assembly and gene annotation are necessary genomic resources for the analysis of functional genomics experiments like ATAC-, ChIP-, or RNA-sequencing. Generally speaking, these data can be acquired from many organisations and in various versions. The majority of bioinformatic workflows demand that users manually input this genomic data, which can be time-consuming and error-prone.
Here, the authors have introduced genomepy, a tool that can find, download, and prepare the appropriate genomic data for your investigation. In order to make an informed choice, Genomepy can search genomic data on NCBI, Ensembl, UCSC, and GENCODE and examine any gene annotations that are accessible. Downloading and preprocessing the chosen genome and gene annotation is possible with logical but configurable settings. Aligner indexes, genomic metadata, and blacklists are a few examples of the additional supporting data that can be automatically generated or downloaded.
For more on genomepy visit https://github.com/vanheeringen-lab/genomepy
Reference:
Frolich S. et. al.(2023) genomepy: genes and genomes at your fingertips. Bioinformatics 39 (3): btad119