I noticed the announcement in NCBI's sra-tools GitHub wiki

With release 2.9.1 of sra-tools we have finally made available the tool fasterq-dump, a replacement for the much older fastq-dump tool.

So I tested the speed from my home.

  1. Just specify a run ID of SRA.
# Just fasterq-dump
% fasterq-dump DRR100656
142.09s user 78.79s system 10% cpu 33:32.82 total

It takes about 33min.

  1. Download SRA-formatted file from DDBJ DRA and dump it.
# Download SRA from DDBJ and then fasterq-dump
% curl -O
% fasterq-dump DRR100657.sra
162.76s user 47.46s system 242% cpu 1:26.76 total

It takes around 5 min to download the file. And the conversion from SRA to FASTQ takes 1.5 min. 242% indicates there was parallel effect!

It was much faster to fetch SRA and then dump it while we have to get the URLs to do so. I regularly get the URLs for that from SRA download links in DBCLS SRA.

Written by bonohu in rnaseq on 土 02 2月 2019.