AgrOmicSo: A client-server interface for accessible large-scale analysis of next-generation sequencing data

Abstract

The analysis of large-scale next-generation sequencing (NGS) data requires substantial computational power, often necessitating the use of high-performance computing (HPC) environments. However, the command-line interfaces for these resources create a significant barrier for many researchers. To bridge this gap, we developed AgrOmicSo (Agri-bio Omics Solution), a software solution designed as a user-friendly interface to a powerful server-side analysis engine. AgrOmicSo’s client-server architecture allows researchers to manage and execute complex, large-scale NGS data analysis pipelines on a remote server directly from an intuitive graphical user interface on their local computer. The software integrates a comprehensive suite of bioinformatics tools for quality control, read mapping, variant calling, and annotation. Notably, it supports three distinct variant calling algorithms—GATK, DeepVariant, and VarScan—offering users flexibility for their specific research needs. AgrOmicSo provides both a “One-Step” mode for rapid, automated batch processing and a “Step-by-Step” mode for detailed, customized analyses. This paper describes the architecture, implementation, and utility of AgrOmicSo as an interface for large-scale genomic analysis, highlighting its potential to advance research by making powerful computational resources more accessible, efficient, and reproducible for a broader scientific community. The client and server program of AgrOmicSo are freely available at https://agromicso.com.