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Welcome to NextGenBench - The Next Generation Sequencing Benchmark System


Introduction:

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:

  • BlastN
  • Bowtie
  • BWA (and all assemblers producing SAM format output (including the MD:Z field (See SAM-format specification)))
  • NextGenMap
  • Shrimp
  • SSaha
NGB is part of the NG* workbench.

Availability:

Requirements:

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

Latest Version NextGenBench 0.0.1 (14th December 2010):

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

 

Download:

  • Source package for Linux are available in gzipped TAR format. The current version of NextGenBench is just tested and released under Linux.
Type Links
Source code NGB.tar.gz
NGB.zip
All-in-one binary release NGB.gz
NGB.zip

Reference:

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

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