New Tool Streamlines Bulk Submission of Sequencing Data to ENA

Researchers have introduced ENflorA, a set of scripts designed to simplify and automate the upload of next generation sequencing data and its accompanying metadata to the European Nucleotide Archive (ENA). The software is described in an open access article published in BMC Bioinformatics on 21 October 2026.

The motivation behind the tool lies in the rapid growth of biological sequence data. As sequencing technologies advance and assembly and annotation tools improve, the volume of data produced by research grows quickly. To keep this data accessible for potential re-analysis, it is typically stored in public online databases such as ENA. According to the authors, the increase in data entails an increase in the time needed for metadata curation and upload.

ENflorA addresses this bottleneck by allowing sample, sequence read and annotated assembly data to be uploaded to ENA in a simple and standardized manner. The tool is intended to reduce the manual effort involved in preparing and submitting large datasets to the public repository.

Metadata entry is handled through spreadsheets, which the developers say makes the process easy and standardized. The software is also suitable for batch upload of data from different sources, meaning submissions that draw on multiple datasets can be handled within a single workflow.

Integration with existing bioinformatic pipelines is another stated feature. ENflorA can be fully integrated into bioinformatic workflows, allowing data submission to become part of the automated processing chain rather than a separate manual step at the end of an analysis.

The tool is platform independent and can be run natively on High Performance Computers. For large files, ENflorA integrates an lftp upload option, and it also includes a test upload option, which allows users to check submissions before committing them to the archive.

According to the authors, by easing the ENA submission process, ENflorA contributes to making high-throughput sequencing data findable, accessible, interoperable and reusable.

The article is published as a software paper in BMC Bioinformatics and is available under open access.

Subject of Research: A software tool for bulk submission of next generation sequencing data and metadata to the European Nucleotide Archive.

Article Title: ENflorA: a flexible tool for the bulk submission of next generation sequencing data to the European Nucleotide Archive

Article References: Alfaro de Prado Martín, A., Fajardo-Gutiérrez, F., de Mestier, A., & Reichel, K. (2026). ENflorA: a flexible tool for the bulk submission of next generation sequencing data to the European Nucleotide Archive. BMC Bioinformatics, 27(1), Article 242. https://doi.org/10.1186/s12859-026-06714-7

Image Credits: AI Generated

DOI: 10.1186/s12859-026-06714-7

Keywords: ENflorA, European Nucleotide Archive, next generation sequencing, data submission, metadata curation, bioinformatics workflows, FAIR data, open access software, high performance computing, BMC Bioinformatics, sequence read archive, batch upload