IDEAL-GENOM: Integrated Downstream Analytical Toolkit for Genomic Analysis

Abstract

There has been an exponential increase in the development of technologies that have offered unprecedented opportunities to unravel the genetic underpinnings of rare and complex diseases. However, despite the progress, and availability of tools, there are still several challenges to over-come, such as the development of a unified framework that facilitates downstream analysis. To address this challenge, we present IDEAL-GENOM (Integrated Downstream Analytical Toolkit for Genomic Analysis), a Python-based wrapper designed to streamline the analytical workflow commonly implemented in genome-wide association studies (GWAS) settings. 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) and GWAS and downstream analysis that will enable beginners and advanced users to leverage the in-built functionalities to per-form GWAS analysis for complex diseases. IDEAL-GENOM is a customizable tool that enables users to efficiently analyze genotyping data with reproducible QC, post-imputation, and GWAS pipelines.