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Peer-reviewedCC BYBMC bioinformatics

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

  • Antonio Alfaro de Prado Martín1
  • Francisco Fajardo-Gutiérrez2
  • Astrid de Mestier1
  • Katja Reichel3
  1. 1Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Altensteinstraße 6, 14195, Berlin, Germany.
  2. 2Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin Luise-Straße 6-8, 14195, Berlin, Germany.
  3. 3Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Altensteinstraße 6, 14195, Berlin, Germany. [email protected].
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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.

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Cite

BibTeXRIS
BibTeX
@article{martin2026enflora,
  title = {{ENflorA: a flexible tool for the bulk submission of next generation sequencing data to the European Nucleotide Archive.}},
  author = {Antonio Alfaro de Prado Martín and Francisco Fajardo-Gutiérrez and Astrid de Mestier and Katja Reichel},
  journal = {BMC bioinformatics},
  year = {2026},
  month = oct,
  doi = {10.1186/s12859-026-06714-7},
  url = {https://europepmc.org/article/MED/42907977},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - ENflorA: a flexible tool for the bulk submission of next generation sequencing data to the European Nucleotide Archive.
AU  - Antonio Alfaro de Prado Martín
AU  - Francisco Fajardo-Gutiérrez
AU  - Astrid de Mestier
AU  - Katja Reichel
PY  - 2026
DA  - 2026/10/21
JO  - BMC bioinformatics
DO  - 10.1186/s12859-026-06714-7
UR  - https://europepmc.org/article/MED/42907977
AB  - 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.
SN  - 1471-2105
ER  -