NSeqVerify: An Easy-to-Use Desktop Suite for Integrated NGS Data Analysis, from Raw Reads to Taxonomic Assignment

Abstract

MotivationThe proliferation of next-generation sequencing (NGS) data has created a computational bottleneck, especially for researchers lacking specialized bioinformatics training. Standard analysis workflows require mastering multiple command-line tools, hindering exploratory data analysis and delaying scientific discovery. ResultsThis work presents NSeqVerify, a new cross-platform, open-source desktop software developed in Java, designed to overcome these barriers. NSeqVerify implements a fully integrated genomic workflow within a single, intuitive graphical user interface (GUI). The suite includes: (1) a preprocessing module for quality control and filtering of FASTQ files; (2) a de novo assembler employing a sophisticated De Bruijn graph algorithm with an iterative multi-k-mer strategy to maximize contiguity; and (3) a taxonomic assignment module that automates BLAST searches against NCBI databases and displays the results in an easily interpretable tabular format. The tool was validated through controlled use cases, demonstrating its ability to accurately reconstruct reference viral genomes (HIV-1) and to deconvolute metagenomic mixtures (HIV-1 and SARS-CoV-2). The final test consisted of analyzing a real elephant fecal virome (SRA: SRR35776009), where NSeqVerify successfully assembled contigs -- two of which overlapped and appeared to form a partial 1555 bp genome of a putative Smacovirus, enabling the identification of its capsid protein and the prediction of its 3D structure using AlphaFold. Conclusion and AvailabilityNSeqVerify democratizes NGS data analysis, providing a robust "all-in-one" solution that empowers molecular biologists, students, and clinicians to perform end-to-end genomic analyses. The software is freely available under the GNU GPLv3 license at (https://github.com/roberto117343/NSeqVerify). Contactroberto117343@gmail.com