DownloadAssemblies - Tutorial

Objective

This tutorial will show you how to download assemblies from NCBI and ENA661K using the DownloadAssemblies module.

Prerequisites

  • NCBI datasets command-line too installed (instructions here).

Procedure

  1. Open a terminal window.

  2. Modify the following command and run it to download assemblies from NCBI and ENA661K:

SR DownloadAssemblies -db NCBI -th 3 --download -fm -o 'path/to/files/DownloadAssemblies_Results' -f '/path/input_table_example.tsv' -e your_email@email.com

Important

The file passed to -f is available here. Do not forget to replace the paths in the command with the paths to the files in your system. Provide your email address to -e.

  1. Check the output directory for the downloaded assemblies.

Example Output Structure

To see the expected output structure, refer to the “Outputs” section in the DownloadAssemblies documentation.