Center for Integrative Bioinformatics Vienna
Max F. Perutz Laboratories
Dr. Bohr Gasse 9
A-1030 Vienna, Austria

Welcome to NGSS - The Next Generation Sequencing Simulation


Next Generation Sequencing Simulation (NGSS) was developed to simulate the process of Next Generation Sequencing. NGSS takes an input sequence and mutates it given a user defined evolutionary distance. NGSS uses the Jukes Cantor model of sequence evolution additionally NGSS allows for insertion and deletion events. This process models on one side the existence of mutants and distance related species, where no reference sequence is available. On the other side it copes with annotation errors in existing reference sequences. The differentiated sequence is than taken as the targeted genome.

In the second step of the simulation, NGSS takes the targeted genome and simulates the sequencing step. All reads are randomly sampled across the entire genome. Per read a sequencing error is applied given a user defined probability.

NGSS was designed to work with Next Generation Sequencing Evaluation (NGSE). This program is required to process the result after the mapping. NGSS and NGSE are part of the Next Generation Sequencing Benchmark System (NGB).

NGSS is part of the NG* workbench.



  • A PC with at least 4 GB of memory and the latest java runtime version

Latest Version NGSS 0.0.1 (14th December 2010):

  • Please read the User Manual carefully before using NGSS the first time or when you upgrade the new version!!



  • Source package for Linux are available in gzipped TAR format. The current version of NGSS is just tested and released under Linux. Further versions will also be available under Windows and Macs.
Type Links
Source code NGSS.tar.gz


The method is described in details in the following articles:
  • Please, let us know if you download this program by sending an email to {fritz.sedlazeck,arndt.von.haeseler}@univie.ac.at

Printable version of: http://www.cibiv.at/software/ngm/NGSBench/NGSS.shtml

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