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

Welcome to NGSE - The Next Generation Sequencing Evaluation System


Next Generation Sequencing Evaluation (NGSE) is designed to evaluate the performance of different mapping programs on the basis of the simulated read set created by Next Generation Sequencing Simulation (NGSS).

NGSE currently supports following mapping programs:

  • BlastN
  • Bowtie
  • BWA (and all assemblers producing SAM format output (including the MD:Z field (See SAM-format specification)))
  • NextGenMap
  • Shrimp
  • SSaha

Next Generation Sequencing Simulation (NGSS). This program simulates the datasets on which the progams operate. NGSS and NGSE are part of the Next Generation Sequencing Benchmark System (NGB).

NGSE is part of the NG* workbench.



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

Latest Version NGSE 0.0.1 (14th December 2010):

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



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

contact imprint .