sra-toolkit

Download data from NCBI-SRA

1. Install sra-toolkit

• From apt-get
  $ sudo apt update
$ sudo apt-get install sra-toolkit

• From source (Installation tutorial)
  $ wget --output-document sratoolkit.tar.gz https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
$ tar -vxzf sratoolkit.tar.gz
$ vi ~/.bashrc

export PATH=$PATH:$PWD/sratoolkit.3.0.0-mac64/bin

$ source ~/.bashrc

Configuration

$ vdb-config -i # -i open the config as interactive mode

Set save file directory as current directory

1. Press "t" to move to the "TOOLS" tab (or press TAB to move one by one and ENTER)
2. Set "prefetch downloads to "current directory"
3. Press "s" followed by "o" to save; press "x" to exit

Or save file directory as user defined directory

1. Press "c" to move to "CACHE"
2. Press "o" to choose location of user-repository; use up & down arrow and ENTER
3. Press TAB to shift to OK tab and press ENTER followed by "y" for yes
4. Press "t" to move to "TOOLS" tab
5. Shift the asterisk to "user-repository"
6. Press "s" followed by "o" to save; press "x" to exit

Download accession list

1. Search for the Bioproject accession number (exp. PRJNA323955) in the NCBI database
2. Click on the SRA link within the top-right "Related information" panel
3. Click on the link "Send results to Run selector"
4. Click on the "Accession List" button within the Download column of the Select panel. Named the accession list as "SRR_Acc_List.txt"

Download FASTQ

Directly download FASTQ

$ for i in `cat SRR_Acc_List.txt`; do
    fasterq-dump ${i};
  done;

Official approach (prefetch + fasterq-dump)

$ mkdir sra
$ for i in `cat SRR_Acc_List.txt`; do
    prefetch --max-size u ${i};
  done;

$ mkdir fastq
$ for j in ./sra/*.sra; do
    fasterq-dump --threads 40 --progress --force -O ../fastq ${j};
  done;