Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim
Peer reviewed, Journal article
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Motivation: The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 base pairs and are thus approaching read lengths obtained from traditional Sanger sequencing. Study design of sequencing projects would benefit from being able to simulate experiments. Results: We explore 454 raw data to investigate its characteristics and derive empirical distributions for the flow values generated by pyrosequencing. Based on our findings, we implement Flowsim, a simulator that generates realistic pyrosequencing data files of arbitrary size from a given set of input DNA sequences. We finally use our simulator to examine the impact of sequence lengths on the results of concrete whole-genome assemblies, and we suggest its use in planning of sequencing projects, benchmarking of assembly methods and other fields. Availability: Flowsim is freely available under the General Public License from http://blog.malde.org/index.php/flowsim/
ECCB 2010 CONFERENCE PROCEEDINGS SEPTEMBER 26 TO SEPTEMBER 29, 2010, GHENT, BELGIUM.