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An efficient simulator of 454 data using configurable statistical models
Fredrik Lysholm1, Björn Andersson, Bengt Persson
1IFM Bioinformatics and SeRC (Swedish e-Science Research Centre), Linköping University, S-581 83 Linköping, Sweden. frely@ifm.liu.se.
BMC Research Notes
|October 28, 2011
Summary
A new tool, 454sim, simulates Roche 454 sequencing data quickly and accurately. This high-speed simulation aids in evaluating bioinformatics algorithms for next-generation sequencing data analysis.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Roche 454 is a prominent second-generation sequencing platform.
- 454 sequence data presents unique challenges for bioinformatics analyses like assembly and alignment.
- Simulating 454 data is crucial for assessing bioinformatics tool performance.
Purpose of the Study:
- To develop a high-speed and accurate simulation tool for Roche 454 sequencing data.
- To provide a platform-independent application for broader accessibility.
- To facilitate rigorous evaluation of bioinformatics algorithms.
Main Methods:
- Developed 454sim, a multi-threaded C++ application.
- Utilized statistical models specific to each Roche 454 chemistry.
- Simulated peak intensities, quality deterioration, and calculated quality values.
- Supported GS20, GS FLX, and Titanium chemistries via external text files.
Main Results:
- 454sim achieves high-speed and accurate simulation of 454 data.
- The tool simulates key data characteristics including peak intensities and quality values.
- Supports all major Roche 454 sequencing generations.
Conclusions:
- 454sim is a novel, platform-independent application for simulating Roche 454 data.
- Offers a significant speed improvement (approx. 200x) over existing methods.
- Enables more efficient and comprehensive evaluation of bioinformatics algorithms.
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