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Related Experiment Video

Updated: Jul 29, 2025

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

GRAPE: genomic relatedness detection pipeline.

Alexander Medvedev^1,2, Mikhail Lebedev², Andrew Ponomarev²

¹Skolkovo Institute of Science and Technology, Moscow, Russian Federation.

|May 24, 2023

Summary

We developed GRAPE, a Genomic RelAtedness detection PipelinE, to accurately classify genetic relatedness. This open-source tool addresses the need for a fast, reliable solution for genomic data analysis in research and commercial applications.

Keywords:

bioinformatics pipeline genetic testing companies genotype identity-by-descent kinship and relationship estimation phasing and imputation sequencing data snakemake workflow

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Accurate relatedness classification is crucial for genomic studies like Genome-Wide Association Studies (GWAS) and genetic linkage analysis.
Unrecognized population structure can lead to false positives in GWAS, impacting research validity.
The direct-to-consumer genetic testing market relies on accurate DNA relative matching services.

Purpose of the Study:

To develop an open-source, end-to-end pipeline for detecting genomic relatedness.
To provide a fast, reliable, and accurate solution for both close and distant kinship.
To integrate necessary processing steps for real-world genotypic data and production readiness.

Main Methods:

Developed GRAPE (Genomic RelAtedness detection PipelinE), an integrated pipeline.
Incorporated data preprocessing, Identity-by-Descent (IBD) segment detection, and relationship estimation.
Utilized software development best practices and Global Alliance for Genomics and Health (GA4GH) standards.

Main Results:

Demonstrated pipeline efficiency on both simulated and real-world genomic datasets.
GRAPE provides a comprehensive solution for genomic relatedness detection.
The pipeline is ready for production integration.

Conclusions:

GRAPE addresses the current gap for an open-source, production-ready relatedness detection pipeline.
The tool enhances the accuracy and reliability of genomic data analysis.
GRAPE facilitates advancements in genetic research and commercial applications.