actapia / download_sra

Download sequence reads from SRA with quality information.

SRA runs downloader

This is a little tool I wrote to download sequence reads in fastq format from the Sequence Read Archive (SRA) without losing quality information.

Requirements

This application has been tested with the following software versions. If you have similar versions, it may still work, but such configurations are untested.

• CPython 3.11
• lxml 4.9.2
• requests 2.28.2
• Bash 5.2.2
• sratoolkit 3.0.0

Usage

With arguments

The script will accept any number of SRA links or accessions as command line arguments. For example,

bash download_sra.sh https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR2321388&display=metadata

or

bash download_sra.sh SRR2321388

If your SRA record is associated with only one run, you can alternatively provide the link to the SRA entry. Hence, the following works.

bash download_sra.sh https://www.ncbi.nlm.nih.gov/sra/SRX1214077[accn]

or

bash download_sra.sh SRX1214077

From stdin

If you need to download many sequence files, you may find it easier to provide a list via standard input. For example,

echo -e "SRX1214077\nSRX1214076" | bash download_sra.sh

Note that download_sra.sh only reads from standard input if no links/accessions are provided as command-line arguments.

Running with multiple jobs

You can provide the -j option to download_sra.sh to make use of multiple processor cores.

bash download_sra.sh -j 4 SRX1214076