Software Open Access
van Heeringen, Simon J
In many analysis workflows, sequencing reads will need to be mapped to a reference genome. Here we present genomepy, a simple software package to automate the download of genomic sequences. It contains both command-line tools as well as a Python API. Supported providers for genomes include UCSC, NCBI and Ensembl. Downloaded genome sequences can be soft- or hard-masked and specific chromosomes or scaffolds can be either included or excluded based on regular expressions. Genomepy is free and open source software and can be installed through standard package managers.