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.
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
|
