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Open Access Technical Note

An efficient simulator of 454 data using configurable statistical models

Fredrik Lysholm1*, Björn Andersson2 and Bengt Persson12

Author Affiliations

1 IFM Bioinformatics and SeRC (Swedish e-Science Research Centre), Linköping University, S-581 83 Linköping, Sweden

2 Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, S-171 77 Stockholm, Sweden

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BMC Research Notes 2011, 4:449  doi:10.1186/1756-0500-4-449

Published: 26 October 2011

Abstract

Background

Roche 454 is one of the major 2nd generation sequencing platforms. The particular characteristics of 454 sequence data pose new challenges for bioinformatic analyses, e.g. assembly and alignment search algorithms. Simulation of these data is therefore useful, in order to further assess how bioinformatic applications and algorithms handle 454 data.

Findings

We developed a new application named 454sim for simulation of 454 data at high speed and accuracy. The program is multi-thread capable and is available as C++ source code or pre-compiled binaries. Sequence reads are simulated by 454sim using a set of statistical models for each chemistry. 454sim simulates recorded peak intensities, peak quality deterioration and it calculates quality values. All three generations of the Roche 454 chemistry ('GS20', 'GS FLX' and 'Titanium') are supported and defined in external text files for easy access and tweaking.

Conclusions

We present a new platform independent application named 454sim. 454sim is generally 200 times faster compared to previous programs and it allows for simple adjustments of the statistical models. These improvements make it possible to carry out more complex and rigorous algorithm evaluations in a reasonable time scale.