TraceTuner, the DNA sequencing quality value, base calling and trace processing software.
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============================================================================= This file is part of TraceTuner, the DNA sequencing quality value, base calling and trace processing software. While providing a flexible interface and the 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. Earlier versions of TraceTuner were used by Celera Genomics to process over 27 million reads from both Drosophila and human genome sequencing 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. ============================================================================= Copyright 1999-2003, Paracel, Inc. All rights reserved. The TraceTuner Software (Copyright 1999-2003, Paracel, Inc. All rights reserved.) (the "Software") is covered by US Patent #6,681,186 and is being made available free of charge by Applera Corporation subject to the terms and conditions of the GNU General Public License, version 2, as published by the Free Software Foundation (the "GNU General Public License"). The Software is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License. The Software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTIES, EXPRESS OR IMPLIED (INCLUDING, WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE). You should have received (LICENSE.txt) a copy of the GNU General Public License along with the Software; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ============================================================================= When referencing this work, please cite the following publication: G.A.Denisov, A.B.Arehart and M.D.Curtin (2004). A system and method for improving the accuracy of DNA sequencing and error probability estimation through application of a mathematical model to the analysis of electropherograms. US Patent 6681186. A journal publication on TraceTuner is currently in preparation.