Install SRA-tools

NCBI SRA files

How to install SRA-tools (fastq-dump, prefetch,... ) on Ubuntu/Linux?

download pages

https://github.com/ncbi/sra-tools/wiki/Downloads

http://ncbi.github.io/sra-tools/fastq-dump.html

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

# create and go to install directory

cd $HOME/tools/sra-tools/

# download latest SRA-tools version (Ubuntu)

curl https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.6/sratoolkit.2.9.6-ubuntu64.tar.gz -o sratoolkit.2.9.6-ubuntu64.tar.gz

# decompress

tar -xvzf sratoolkit.2.9.6-ubuntu64.tar.gz

# check directory name (sra-tools version)

ls

sratoolkit.2.9.6-ubuntu64/

sratoolkit.current-ubuntu64.tar.gz

# add location to system PATH (using current version directory name)

export PATH=$HOME/tools/sra-tools/sratoolkit.2.9.6-ubuntu64/bin:$PATH

# check installation

fastq-dump --help

fastq-dump -V

fastq-dump : 2.9.6

SRA download directory

fastq-dump & prefetch will save the downloaded .sra files in

$HOME/ncbi/public/sra/

Change the default SRA download directory by using

→ sratoolkit configuration

https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration