IDEAL-GENOM: integrated downstream analytical toolkit for genomic analysis

Abstract

Abstract There has been an exponential increase in the development of technologies that have offered unprecedented opportunities to unravel the genetic underpinnings of complex traits. However, despite the progress and availability of tools, there are still several challenges to overcome, such as the development of a unified framework that facilitates downstream analysis. To address this challenge, we present IDEAL-GENOM (Integrated Downstream Evaluation And anaLysis toolkit for GENOMic data), a Python-based wrapper designed to streamline the analytical workflow commonly implemented in binary (case-control) genome-wide association studies (GWAS). IDEAL-GENOM integrates widely used tools such as PLINK, GCTA, and bcftools along with custom-developed functionalities, enabling reproducible results through parameter sharing. IDEAL-GENOM provides a simplified framework for quality control (QC), GWAS, and downstream analysis that will enable beginners and advanced users to leverage the built-in functionalities to perform GWAS analysis for complex traits with binary outcomes. IDEAL-GENOM is a customizable tool that enables users to efficiently analyze genotyping data with reproducible QC, post-imputation, and GWAS pipelines.