Short script used to download, rename and gzip SRA FASTQ files from Accession List.
It requires a comma-delimited table containing SRR numbers in the first column, and desired corresponding filename in the second column (See Example_SRR_List.csv).
The workflow is encoded in Shell language and is supposed to be launched under a Linux environment. Moreover, it was written to be used on a computing cluster with tools already pre-installed in the form of modules. Modules are so loaded using module load <tool_name> command. If you use manually installed environments, simply replace module loading in the script section by the environment activation command.
The provided script launch downloading tasks as qsub task submission.
Name Version
sra-tools 2.11.0
sh DL_SRA.sh <sheet_sample.csv>