IDEAL-GENOM: integrated downstream analytical toolkit for genomic analysis
- 1Centre for Genetic Epidemiology, Universitätsklinikum Tübingen , Silcherstraße 5, Tübingen 72076, Baden-Württemberg ,
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.
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BibTeX
@article{ricardo2026idealgenom,
title = {{IDEAL-GENOM: integrated downstream analytical toolkit for genomic analysis}},
author = {Luis Giraldo González Ricardo and Amabel M M Tenghe and Ashwin Ashok Kumar-Sreelatha and Manu Sharma},
journal = {G3: Genes, Genomes, Genetics},
year = {2026},
month = oct,
doi = {10.1093/g3journal/jkag283},
url = {https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag283/8916423},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - IDEAL-GENOM: integrated downstream analytical toolkit for genomic analysis
AU - Luis Giraldo González Ricardo
AU - Amabel M M Tenghe
AU - Ashwin Ashok Kumar-Sreelatha
AU - Manu Sharma
PY - 2026
DA - 2026/10/14
JO - G3: Genes, Genomes, Genetics
DO - 10.1093/g3journal/jkag283
UR - https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag283/8916423
AB - 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.
SN - 2160-1836
ER -