Sequence read archive and other tools

To download and analyze SRA data, some protocol is needed. Here I describe the usual protocol to do the analysis.

(update of 21 February 2021)

If you use Linux (Ubuntu)
(WSL is also applicable)


Use Conda

conda install -c bioconda parallel-fastq-dump

or Python pip

pip install parallel-fastq-dump

or Debian package repoditory

Open terminal
Install SRA toolkit by command:

$sudo apt-get install sra-toolkit

Input your password
Write Y when asked
Choose OK if some violet dialog box appears
SRA-toolkit is installed on your computer.

or download from the website

$wget url (from

To check whether SRA-toolkit is already installed or not:

$prefetch --help

HTTP download sometimes has trouble so FASP is better for download a high amount of data.

Download ASPERA connect
Choose Linux installation

Extract file

$tar -xvzf ibm-aspera-connect-3.x.x.17xxxx-linux-g2.12–64.tar.gz

Install file

$bash ibm-aspera-connect-3.x.x.17xxxx-linux-g2.12–

add ascp to the path
open .bashrc file using nano or vim text editor
write the following at the end of the text
export PATH=/home/hendra/.aspera/connect/bin:$PATH
change hendra with your user name

Download from AWS is now available through HTTPS so using wget is also fast.

Single-end sequencing result

fastq-dump <SRA.sra>
fastq file checked by fastqc

Paired-end sequencing result

$ fastq-dump --split-files <SRA.sra>#this will results in two file with name like:
#SRA_1.fastq and SRA_2.fastq


(To check fastq data quality)
Still in terminal

$ sudo apt-get install fastqc


(To trim data)

$ sudo apt-get install ea-utils

or from

$ wget

TCR/BCR sequence extraction


Download mixcr (in zip file) from release page in Github:

$ wget
$ unzip

add mixcr to the path
open .bashrc using nano or vim text editor
write the following at the end of the text
export PATH

To check the functionality of each software, we can do :
$ mixcr — help
(use a double hyphen before help)
This can be applied to other software as well

Alignment and gene expression analysis




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