Center for Integrative Bioinformatics Vienna
Max F. Perutz Laboratories
Dr. Bohr Gasse 9
A-1030 Vienna, Austria
Welcome to NextGenBench - The Next Generation Sequencing Benchmark System
The central elements of NextGenBench are two programs Next Generation Sequencing Simulation (NGSS) and Next Generation Sequencing Evaluation (NGSE). 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.
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:
Latest Version NextGenBench 0.0.1 (14th December 2010):
Reference:The method is described in details in the following articles: