Basecalling with LifeTrace

Genome Research
D WaltherM Morris

Abstract

A pivotal step in electrophoresis sequencing is the conversion of the raw, continuous chromatogram data into the actual sequence of discrete nucleotides, a process referred to as basecalling. We describe a novel algorithm for basecalling implemented in the program LifeTrace. Like Phred, currently the most widely used basecalling software program, LifeTrace takes processed trace data as input. It was designed to be tolerant to variable peak spacing by means of an improved peak-detection algorithm that emphasizes local chromatogram information over global properties. LifeTrace is shown to generate high-quality basecalls and reliable quality scores. It proved particularly effective when applied to MegaBACE capillary sequencing machines. In a benchmark test of 8372 dye-primer MegaBACE chromatograms, LifeTrace generated 17% fewer substitution errors, 16% fewer insertion/deletion errors, and 2.4% more aligned bases to the finished sequence than did Phred. For two sets totaling 6624 dye-terminator chromatograms, the performance improvement was 15% fewer substitution errors, 10% fewer insertion/deletion errors, and 2.1% more aligned bases. The processing time required by LifeTrace is comparable to that of Phred. The predicted quality s...Continue Reading

References

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Citations

Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Andy WildenbergPavel Sumazin
Feb 26, 2008·Bioinformatics·Ketil Malde
Feb 22, 2003·Nucleic Acids Research·Jean-Claude Nicod, Carlo R Largiadèr
Jan 24, 2008·Genome Research·William BrockmanDavid B Jaffe
Jun 3, 2009·Journal of Gastroenterology and Hepatology·Yue HanXin Xin Zhang
Dec 6, 2002·Genome Research·Zhengyan KanWarren Gish

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