WORKSHOP: Retrieving nucleotide sequencing data from the European Nucleotide Archive

This record includes training materials associated with the Australian BioCommons workshop ‘Retrieving nucleotide sequencing data from the European Nucleotide Archive’. This workshop took place on 3 April 2025.

Event description

The European Nucleotide Archive (ENA) is the European node of the International Nucleotide Sequence Database Collaboration (INSDC), providing a comprehensive record of the world’s nucleotide sequencing information, covering raw read sequencing data, sequence assembly information and functional annotation. The three INSDC members (ENA, NCBI-SRA and DDBJ-SRA) routinely exchange data which ensures nucleotide data is archived and shared across geographically dispersed locations (Europe, USA and Japan). The ENA is provided by EMBL’s European Bioinformatics Institute, EMBL-EBI.

This workshop provides an introduction to the ENA data and metadata model and data retrieval tools, followed by an opportunity to practice retrieving a range of different data types from the ENA using a variety of tools and protocols.

Lead trainers: 

• Dr Joana Pauperio, Biodiversity Curator, European Nucleotide Archive, EMBL-European Bioinformatics Institute

• Maira Ihsan, User Support Bioinformatician, European Nucleotide Archive, EMBL-European Bioinformatics Institute

Training materials

Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.

Files and materials included in this record:

• Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.

• ENA_data_retrieval_slides (PDF): Slides that introduce the ENA metadata model and provide an overview of methods of data retrieval from the ENA

• ENA_data_retrieval_practical (PDF): A practical guide that provides step by step instructions on how to retrieve data from the ENA