Work

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

Year: 2026

Type: article

Abstract: BACKGROUND: With the advancement of sequencing technologies and increasing quality of assembly and annotation tools, the amount of biological sequence data produced by research grows rapidly. To keep this data accessible for potential re-analysis, it is typically stored in public online databases, such as the European Nucleotide Archive (ENA). However, the increase in data entails an increase in time needed for metadata curation and upload. We propose a tool to simplify and automatize the upload of experimental and metadata to public repositories. RESULTS: We developed ENflorA, a set of scripts by which sample, sequence read and (annotated) assembly data can be uploaded to ENA in a simple and standardized manner. Our software allows easy metadata entry via spreadsheets, is suitable for batch upload of data from different sources, and can be fully integrated in bioinformatic workflows. It is platform independent and can be run natively on High Performance Computers, integrates an lftp upload option for big files and a test upload option. CONCLUSIONS: By easing the ENA submission process, ENflorA contributes to making high-throughput sequencing data findable, accessible, interoperable and reusable.

Source: BMC Bioinformatics

DOI: 10.1186/s12859-026-06714-7

Authors: Antonio Alfaro de Prado Martín, Francisco Fajardo-Gutiérrez, Astrid de Mestier, Katja Reichel

Institutions: Freie Universität Berlin, Botanic Garden and Botanical Museum Berlin

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,990

Funders: Freie Universität Berlin, Leibniz-Institut für Zoo- und Wildtierforschung, Leibniz-Gemeinschaft