Abstract
BackgroundRoche 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.FindingsWe 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.ConclusionsWe 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.
Highlights
The introduction of 2nd generation sequencing techniques has resulted in a myriad of new large DNA sequencing projects, many of which have posed new challenges for bioinformatics
The 454 instruments use a type of pyrosequencing chemistry, where the complementary strand is elongated through repeated cycles, each using one of the four nucleotides
The complementary strand is elongated in the absence of a terminator, and homopolymer lengths are estimated by the light intensity recorded
Summary
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. 454sim is generally 200 times faster compared to previous programs and it allows for simple adjustments of the statistical models. We present a new platform independent application named 454sim. These improvements make it possible to carry out more complex and rigorous algorithm evaluations in a reasonable time scale
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call