fasterq-dump
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 olderfastq-dumptool.
So I tested the speed from my home.
- 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.
- Download SRA-formatted file from DDBJ DRA and dump it.
# Download SRA from DDBJ and then fasterq-dump
% curl -O ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sra/ByExp/sra/DRX/DRX094/DRX094089/DRR100656/DRR100656.sra
% 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.