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.
This series is designed with flexibility in mind. You can apply to attend one or more workshops - choose the workshop(s) most relevant to you.
| Date/Time | Workshop title | Dataset | Submission route |
|---|---|---|---|
| 25 March 2025 1 - 4 pm AEDT |
Submitting raw read sequencing data using interactive web-based tools | Raw reads | Interactive web-based submission |
| 26 March 2025 1 - 4 pm AEDT |
Submitting raw read sequencing data using programmatic tools | Raw reads | Programmatic submission |
| 27 March 2025 1 - 3 pm AEDT |
Submitting raw-read sequencing data using command line based tools | Raw reads | Command-line submission |
| 31 March 2025 1 - 4 pm AEDT |
Submitting genome assembly and annotation data using the command line | Genome assembly and annotation data | Command-line submission |
| 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 | Environmental DNA (eDNA) | Multiple methods in development |
Learning outcomes:
By the end of each workshop you should be able to:
Identify the importance of data sharing
Outline the purpose of the ENA
Explain the ENA Metadata Model and the importance of metadata
Describe the data submission routes at the ENA
Identify the range of tools and services offered by the ENA for data submission
Submit the demonstrated data type using the ENA submission route shown in the workshop(s) you attend
Location: Online via Zoom.
Date/Time: 25 March to 3 April 2025. All times are provided in AEDT (Melbourne). Check the start time at your location.
Lead Trainers:
Maira Ihsan, User Support Bioinformatician, European Nucleotide Archive, EMBL-European Bioinformatics Institute
Dr Joana Pauperio, Biodiversity Curator, European Nucleotide Archive, EMBL-European Bioinformatics Institute
Who these workshops are for:
This series of related workshops is for Australian-based life scientists and bioinformaticians who are working with nucleotide sequencing data and who would benefit from submitting their data to the INSDC.
Prerequisites:
You must be associated with an Australian organisation to participate in these workshops.
Interactive submission routes: none
Programmatic submission routes: some understanding of XML and JSON file formats is recommended
Command line submission route: a basic understanding of how to interact with the command line is required
How to join:
Attendance at these workshops is fully subsidised, but registrations are essential.
You can apply to attend one or more workshops - choose the workshop(s) most relevant to you on the registration form.
Details on how to join and essential preparation steps will be provided closer to the date of the workshops.
This event is part of a series of bioinformatics training events. If you’d like to hear when registrations open for other events, please subscribe to the Australian BioCommons newsletter.