TraceTuner
Overview
TraceTuner is a DNA sequencing quality value, base calling and trace processing software application originally developed by Paracel, Inc. While providing a flexible interface and capability to adopt the “pure” base calls produced by Phred, KB or any other “original” caller, it offers competitive features not currently available in other tools, such as customized calibration of quality values, advanced heterozygote and mixed base calling and deconvolving the “mixed” electropherograms resulting from the presence of indels into a couple of “pure” electropherograms. Previous versions of TraceTuner were used by Celera Genomics to process over 27 million reads from both Drosophila and human genome projects and by Applied Biosystems, as a component of its SNP detection and genotyping software product SeqScape. TraceTuner implements an advanced peak processing technology for resolving overlapping peaks of the same dye color into individual, or “intrinsic” peaks. This technology was protected by US Patent #6,681,186. Currently, TraceTuner is an open source software, which has been used by J. Craig Venter Institute’s DNA Sequencing and Resequencing pipelines.