aandradebio / getSRAdata

Simple code to retrieve reads from the SRA database

SRA Data Downloader

This script automates the process of downloading data from the Sequence Read Archive (SRA) based on a list of BioProject IDs.

Usage

1. Ensure you have the necessary tools installed: prefetch, fasterq-dump, pigz.

2. Create a file named PRJNA.txt containing BioProject IDs, with each ID on a new line.

3. Run the script using the following command:

   ./download_data.sh

Script Overview

The script performs the following steps:

• Reads BioProject IDs from a file (PRJNA.txt).
• Creates a folder for each BioProject.
• Fetches SRR accession numbers for each BioProject.
• Downloads data for each SRR accession in parallel, using prefetch, fasterq-dump, and pigz.

Requirements

• prefetch
• fasterq-dump
• pigz

Notes

• The script assumes that you have the required tools installed and configured.
• The data will be downloaded to the same directory where the script is executed.

Feel free to customize the script and this README according to your specific needs.

Author

Amanda Araújo Serrão de Andrade [e-mail]

Feel free to contact me, open an issue, or a pull request.