Entering edit mode
7.6 years ago
flight029000
•
0
How to download a 100 fastq files at once using SraToolkit fastq-dump? Is there any software with GUI or shell codes published somewhere?
use GNU parallel
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
No, that is not recommended for this type of job! As fastq-dump is mainly a downloader, the limiting factor is mostly network bandwidth and IO. Unless you have a much larger bandwidth on your side than NCBI's load balancer is willing to assign to your ip for each connection, it is most likely to be slower with so many connections. It depends on how their load balancing is implemented but you might even be throttled or blacklisted. I would try max. 4-6 parallel downloads and monitor the network traffic.
Did you try using a for loop already?
no, post an example, pls
What did you try already?