H3NGST: a fully automated, web-based platform for end-to-end ChIP-seq analysis

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely used technique for mapping protein-DNA interactions and histone modifications across the genome. Despite its utility, current analysis tools often require manual file processing, rigid input formats, and a significant level of bioinformatics expertise, posing a challenge for many experimental researchers. We present H3NGST (Hybrid, High-throughput, and High-resolution NGS Toolkit), a fully automated and user-friendly web-based platform for ChIP-seq analysis. H3NGST streamlines the entire analysis workflow, including raw data retrieval via BioProject ID, quality control, adapter trimming, reference genome alignment, peak calling, and genomic annotation. The system also categorizes peaks by genomic region, such as promoters. With minimal user input, H3NGST provides high resolution and reproducible results for both transcription factor binding and histone modification studies. H3NGST significantly reduces the technical barriers to ChIP-seq analysis by eliminating the need for local installations, programming skills, or large file uploads. Its intuitive web interface and mobile accessibility extend its usability to researchers with different computational backgrounds. The platform is scalable for high-throughput studies and is freely available at https://ngschiphhh.duckdns.org .