SRA-Toolkit and fasterq-dump on the HPC cluster

fastq-dump and fasterq-dump are both used to extract data in the FASTQ or FASTA format from SRA-accessions.

fasterq-dump is the successor to fastq-dump.  It is faster (surprise) and uses temporary files and multi-threading to speed up the extractions of files.

For best performance, it is recommended to use prefetch to download the accession before using fasterq-dump.  The prefetch tools downloads all necessary files and can resume interrupted downloads.

From either bamdev1 or bamdev2:

Quick test:

1. Create an empty directory (named whatever) that will be used for your local repository.

2. Follow the instructions here

Download data

👉 Some of the data sets are large; ensure you have enough space

👉 When changing the local repository, ensure to re-run `vdb-config`

👉 Use `vdb-validate` to test downloaded data for integrity

Robert Petkus, 9/1/23