XSXS: a FASTQ read simulator


XS is a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. XS handles Ion Torrent, Roche-454, Illumina and ABI-SOLiD simulation sequencing types. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores). Quality-scores can be simulated using uniform and Gaussian distributions.


Pratas, D., Pinho, A. J., & Rodrigues, J. M. R. (2014). XS: a FASTQ read simulator. BMC research notes, 7(1), 40.

Web download
Download and install from console
wget https://github.com/pratas/xs/archive/master.zip
unzip master.zip
cd xs-master

Or alternatively:

wget http://bioinformatics.ua.pt/wp-content/uploads/2014/02/XS.tar.gz
tar -vzxf XS.tar.gz
cd XS