The fastest way to download a list of SRR accessions from Sequence Read Archive with sratoolkit
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16 months ago
Denis ▴ 200

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.

sequence genome • 1.5k views
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16 months ago
GenoMax 101k

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

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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.

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8 weeks ago

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

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