Question: The fastest way to download a list of SRR accessions from Sequence Read Archive with sratoolkit
0
gravatar for Denis
12 months ago by
Denis200
Denis200 wrote:

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 • 843 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by Denis200
1

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

ADD REPLYlink written 12 months ago by GenoMax95k
1

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.

ADD REPLYlink modified 12 months ago • written 12 months ago by ATpoint44k
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