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eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts.

Praveen Krishna Chitneedi¹, Frieder Hadlich¹, Gabriel C M Moreira²

¹Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.

NAR Genomics and Bioinformatics

|September 25, 2024

Summary

This summary is machine-generated.

This study developed a Nextflow pipeline for expression quantitative trait loci (eQTL) analysis, simplifying complex bioinformatics workflows. The pipeline efficiently handles large-scale Next-generation sequencing data and resource sharing for eQTL studies.

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Area of Science:

Genomics
Bioinformatics

Background:

Next-generation sequencing (NGS) data analysis pipelines are increasingly complex.
Orchestrating these pipelines with traditional Bash scripts is challenging.
Bioinformatics workflow managers like Nextflow offer solutions for complex data analysis.

Purpose of the Study:

To develop a modular and shareable bioinformatic pipeline for expression quantitative trait loci (eQTL) detection using Nextflow.
To address the computational and data access challenges in large-scale eQTL studies.

Main Methods:

Utilized Nextflow, a bioinformatics workflow manager.
Developed the pipeline using Nextflow's DSL2 modular syntax.
Tested the pipeline with pilot data to assess runtime and resource requirements.

Main Results:

The developed Nextflow pipeline demonstrated suitability for large-scale eQTL analyses.
The pipeline's modular design facilitates sharing of computational resources and data access.

Conclusions:

Nextflow provides an effective framework for managing complex bioinformatics pipelines.
The new pipeline is a valuable tool for efficient and scalable eQTL studies.