NGSDataBooster: Simplifying and democratizing the open deposition of Next Generation Sequencing Data
Category
Contribute
Institutions
ETH Zurich
Data type
Genomic data
Field
Life sciences
Researchers
Rehrauer, Hubert
Description
The Gene Expression Omnibus (GEO) is a major public database where scientists deposit genomics data so it can be reused by others. Although essential for transparency and reproducibility, submitting data to GEO has traditionally been a slow and technically demanding process. Researchers must manually upload large files, generate file integrity codes (MD5 checksums), and complete complex metadata forms. These steps often take several hours, are error-prone, and usually require specialized bioinformatics expertise, creating barriers for many scientists. To address this challenge, we developed and operate the GEO Uploader, a user-friendly web service that automates the entire submission workflow. With just a few clicks, researchers can upload files, generate checksums, and complete metadata templates. Progress is tracked in real time, and the tool prevents common errors by pre-filling technical details automatically. The GEO Uploader has already been adopted by more than 30 researchers, who successfully used it for over 60 data uploads, including datasets larger than 500 gigabytes. Because it requires no advanced computing skills, it enables a much broader community to share data independently. By making GEO submissions faster, easier, and more reliable, the GEO Uploader lowers barriers to open science and supports wider adoption of reproducible research practices.