Question: What is the fastest way to download all SRA files of a SRA Study?
0
gravatar for lokdeep17
4 weeks ago by
lokdeep170
lokdeep170 wrote:

I want to download all the SRA files in an SRA study (usually named as SRPXXXXX). One way to do this is to download using a "For loop", but that is slow. Does someone know a better, and faster way to download all the SRA files in an SRA study?

ADD COMMENTlink modified 4 weeks ago by ATpoint14k • written 4 weeks ago by lokdeep170
3
gravatar for ATpoint
4 weeks ago by
ATpoint14k
Germany
ATpoint14k wrote:

Download them from the European Nucleotide Archive using Aspera and GNU parallel, see Fast download of FASTQ files and metadata from the European Nucleotide Archive (ENA).

Alternatively, if you want to stick with NCBI, make a list with accessions, line:

SRRXXXXX1
SRRXXXXX2
SRRXXXXXn

install GNU parallel and then use cat accessions.txt | parallel -j $JOBS "prefetch {}". In any case, install Aspera for faster download. See the NCBI documentation on it.

where $JOBS is the number of parallel downloads, depending on your I/O capacity. This can then be converted to fastq wth fastq-dump or (my recommendation) parallel-fastq-dump.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by ATpoint14k
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