Welcome to NGSS - The Next Generation Sequencing Simulation
Introduction:
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.
Availability:
Requirements:
- 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!!
Download:
- 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.
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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