The fastest way to download a list of SRR accessions from Sequence Read Archive with sratoolkit

Question

[Denis]

I've installed sratoolkit.2.10.0 at my home on a cluster. I have to download a numerous SRR accessions to my home directory. There are a several options, as i can understand:

1. fastq-dump
2. run prefetchutility, then convert resulted sra files to fastq by fastq-dump
3. fasterq-dump (able to use multi-threading, but if i'm correct can not employ list of SRR accessions as input)

Which option is the fastest? Could you please provide a command line example which will be suitable for my purposes?

I've found very useful a post here: download from SRA However it seems too old.

Answer 1

[GenoMax]

Your best bet is to use this: Fast download of FASTQ files from the European Nucleotide Archive (ENA) instead.

[ATpoint]

This link covers the (in my opinion) two fastest options. The first is to download directly in fastq format from ENA, and the second is prefetch followed by parallel-fastq-dump. See the thread for details including code examples. Don't use any of the "dump" commands to download data directly, too slow and too unstable in my experience.

Answer 2

[kostaspildish]

Assuming you are using bash, you can employ an accession list (or any text file with accessions separated by returns) for faster-dump as follows: cat SraAccList.txt | xargs fasterq-dump - this also takes parameters eg --outdir