Download FASTQ files from ENA

A component to download a set of FASTQ files under a certain project/study/experment by providing an accession ID from the European Nucleotide Archive (ENA). The component works by first getting a summary table of samples belonging to the provided accession number. In this summary table are paths (ftp) to zipped FASTQ files of individual samples.
Using these paths, zipped FASTQ files are downloaded and stored under a directory named data/ inside

Supported accession types are Projects, Studies, BioSamples, Samples, Experiments, Runs and Analyses. Refer to https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html to see details. The component is able to handle both single and paired library layouts in a seamless fashion.

Note:
Files will not be downloaded if their up-to-date version already exists under data/.

Options

Accession ID
The accession ID of samples. This could be either the study or submission accession. Multiple fastq files can be submitted under the same submission ID to EBI. [e.g. PRJDB5238, SRX103293]

Input Ports

This node has no input ports

Output Ports

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Table containing the list of files that have been transferred and if they have been transferred or were already up to date. If files are allowed to fail there is an additional column, that will indicate if the transfer was successful or did fail.

Nodes

Extensions

Links

Download

To use this component in KNIME, download it from the below URL and open it in KNIME:

Download Component
On NodePit since: 2025-03-25
Last update: 2026-01-31
Created with KNIME version: v4.1.2

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