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

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.