Download Samples

Data download options

There are multiple methods to retrieve sequencing data, from simple tools like NCBI’s Galaxy to the relatively more complex, Linux CLI. Shotgun metagenomics often generates substantial data, so be prepared for a sizable download. Several tools are available for you to access metagenomic data. Select the method that aligns with your familiarity and preferences, ensuring you have the necessary software (like the SRA Toolkit) installed if you opt for command-line downloading.


NCBI’s Sequence Read Archive

Directly accessible via the NCBI website, providing a straightforward approach to retrieve sequencing data.


Provides a user-friendly interface for both data retrieval and analysis, simplifying the process.

Cloud Delivery

Utilizes cloud services for streamlined and scalable data retrieval, offering efficiency and scalability in handling large volumes of data.

Linux CLI

A method that requires obtaining the accession list first for efficient downloading via the command line, suitable for users comfortable with command-line operations.

Follow along

You can locate relevant data by referencing a specific paper you’re interested in and checking the availability of the data. Let’s consider PRJNA834801. This public study by Dr. Wallen and their team covering Parkinson’s disease will be used as an example.

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