General Guide on ENA Data Retrieval

Welcome to the general guide for the European Nucleotide Archive data discovery and retrieval. Please take some time to view this introduction and explore all the options available for our data retrieval services.

Viewing and Exploring ENA Records

The table below summarises the domains of data held within ENA and example records that are archived within each domain and displayed within the ENA Browser. Please see our How To guide on exploring an ENA project for an example of how to navigate through an ENA Project in the browser:

Data Domain Description Example Records
Contains information on a biological
research project. This holds all the
data generated as part of this
PRJEB1787 (ERP001736)
Represents biological samples
collected and sequenced in real life
SAMEA2620084 (ERS488919)
Hold raw read files and sequencing
Hold results files of analyses
performed on sequencing data and
analysis methods
Contig set
Hold contig sets generated as part of
a genome or transcriptome assembly.
Represents an entire genome assembly
and holds any contig sets or sequence
records generated as part of the
Sequences (*)
Any sequence records from coding or
non-coding regions to full assembled
The sequenced organism or metagenome
of a sample
Sample Checklist
The checklist of metadata that the
sample was registered with

* Assembled and annotated sequence records fall into different data classes. Read more about the different classes of sequences here.

Search and Retrieval

You can search across the ENA browser in a number of ways:

The advanced search in the browser provides a simple interface for building more complex search queries that can be saved and run again with Rulespace. See our step by step guide on how to use the advanced search for examples on how to build queries and how to use Rulespace:

The ENA Browser also provides different means to download data from the archive whether its XML ENA records, a tabulated summary of metadata resulting from a search or sequencing data files submitted as part of a research project. See our guide on file download for details on how to use our data retrieval services to download data from the archive:

Programmatic Access

When working with a large number of records or when developing an automated pipeline, it can be preferable to explore and interact with the programmatic services that ENA has to offer.

Once you are familiar with how ENA records are linked and what data are available associated with each record, please explore our more advanced guides foraccessing data from the archive programmatically: