Download mutiple SRA files in linux

Question

[Leo]

Good day all,

I have to donwload a lot of metagenomic source sequence which have been deposited in SRA by using 'prefetch' command in linux platform, but the 'prefetch' command only allow to donwload one sequence per time, may i know any command which will allow to download multiple SRA sequence at once.

Thanks for reply.

Answer 1

[dan.shea]

NCBI has instructions on how to use the ascp utility to download items. I've used it in the past for bulk downloads.

[Leo]

Thanks for your reply.

NCBI did provided the information to download a bulk of file by using ascp, but it did not state the command and only the command to download a single file is provided: [path_to_ascp_binary]/ascp -i [path_to_Aspera_key]/asperaweb_id_dsa.openssh -k 1 –T -l200m [e-mail]:/sra/sra-instant/reads/ByRun/sra/SRR/SRR304/SRR304976/SRR304976.sra [local_target_directory]

Can you explain more? Thanks.

[GenoMax]

@Leo: If you have a list of SRA #'s run a loop (to go through that list) using ascp (or even prefetch) command. How to run a batch .sra to .fastq processing loop using linux bash?