KhufuEnv, an auxiliary toolkit for building computational pipelines for plant and animal breeding

BACKGROUND: In the era of short- and long-read sequencing, vast amounts of DNA sequencing data are being generated. While a variety of tools exist for analyzing and manipulating genomics data, many have a finite number of functions, and thus, require users to depend on multiple sources for conducting analyses and processing data. An integrative environment of tools which is accessible to users of different computational backgrounds would facilitate more efficient data processing and level the playing field for researchers whose research depends on analyzing genomic data. RESULTS: We developed the KhufuEnv, an open-source, auxiliary environment for manipulating and analyzing genomic and other datasets. As a proof of concept, we demonstrate rapid de novo identification of previously characterized quantitative trait loci (QTL) for cold tolerance in peanut and hairlessness in dog and a candidate sex-determination region (SDR) in Amborella trichopoda and calculate the proportion of the genome containing runs of homozygosity (ROH) in canine using previously published datasets. CONCLUSIONS: We introduce the KhufuEnv, which provides buildable tools for generating custom pipelines for analyzing a variety of genomic datasets from different species. The KhufuEnv is an open-source auxiliary environment available at https://github.com/w-korani/KhufuEnv. Its tools can be exploited for numerous applications and implemented for quick analysis supporting users with minimal computational experience.