WORKSHOP SERIES: Submitting sequencing data and genome assemblies to the European Nucleotide Archive

This record includes training materials associated with the Australian BioCommons workshop series ‘Submitting sequencing data and genome assemblies to the European Nucleotide Archive. These workshops took place between 25 March - 2 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 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.

ENA team members Dr Joana Pauperio and Maira Ihsan will deliver a series of related workshops on submitting raw read sequencing, Metagenome-Assembled Genome (MAG), environmental DNA (eDNA) and genome assembly and annotation data to ENA. 

Each workshop will begin with an introduction to the ENA data and metadata model. You will then be guided through hands-on exercises using example data sets to practice data submission via one of three submission routes:

• Interactive web-based submission: these are completed by filling out web forms in your browser and downloading template spreadsheets that can be completed off-line and uploaded to ENA. 

• Command-line based submission: Data submissions of this type are completed via the command line using ENA's bespoke Webin-CLI program. This validates your submissions entirely before you complete them, allowing you maximum control of the process. Webin-CLI is the only way to submit assembled genomes and transcriptomes.

• Programmatic submission: these are completed by preparing your submissions as XML/JSON documents and either sending them to ENA using a program such as cURL or using ENA's Webin Portal

Workshops in this series include:

• 25 March 2025, 1 - 4 pm AEDT: Submitting raw read sequencing data using interactive web-based tools

• 26 March 2025, 1 - 4 pm AEDT: Submitting raw read sequencing data using programmatic tools

• 27 March 2025, 1 - 3 pm AEDT: Submitting raw-read sequencing data using command line based tools

• 31 March 2025, 1 - 4 pm AEDT: Submitting genome assembly and annotation data using the command line

• 1 April 2025, 1 - 4 pm AEDT: Submitting Metagenome-Assembled Genome (MAG) data to ENA and MGNify using the command line Metagenome-Assembled Genome (MAG) Command-line submission

• 2 April 2025, 1 - 4 pm AEDT: Submitting environmental DNA (eDNA) data

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 series of workshops including, description, event URL, learning objectives, prerequisites, technical requirements etc.

Each workshop in this series has:

• Slides that introduce the ENA metadata model and provide an overview of the submission process and/or type of data that is the focus of the workshop.

• A practical guide that provides step by step instructions on how to submit data

Submitting raw read sequencing data using interactive web-based tools

• Slides: ENA_submission_interactive_slides.pdf

• Practical: ENA_submission_interactive_practical.pdf

Submitting raw read sequencing data using programmatic tools

• Slides: ENA_submission_programmatic_slides.pdf

• Practical: ENA_submission_programmatic_practical.pdf 

Submitting raw-read sequencing data using command line based tools

• Slides: ENA_submission_commandline_slides.pdf

• Practical: ENA_submission_commandline_practical.pdf

Submitting genome assembly and annotation data using the command line

• Slides: ENA_submission_assemblies_annotations_slides.pdf

• Practical: ENA_submission_assemblies_annotations_practical.pdf

Submitting Metagenome-Assembled Genome (MAG) data to ENA and MGNify using the command line Metagenome-Assembled Genome (MAG) Command-line submission

• Slides: ENA_submission_MAGs_slides.pdf

• Practical: ENA_submission_MAGs_practical.pdf

Submitting environmental DNA (eDNA) data

• Slides: ENA_submission_eDNA_slides.pdf

• Practical: ENA_submission_eDNA_practical.pdf