tracetuner - 3.0.6~beta+dfsg-3 main

Tracetuner is a tool for base and quality calling of trace files from
DNA sequencing instruments.
Traditional DNA sequencing yields curves from four different
channels or light frequencies that human or (preferably) machines
are interpreting to determine the actual base (A,C,G or T) and
the confidence with which this is determined.
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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.
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Later versions
Previous versions of TraceTuner were used by
Celera Genomics to process over 27 million reads from both Drosophila
and human genome projects.
In 2000, Applied Biosystems
bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the
customers of these capillary electrophoresis sequencers.
its SNP detection and genotyping software product SeqScape.
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TraceTuner implements an advanced peak processing technology for resolving
overlapping peaks of the same dye color into individual, or "intrinsic"
peaks. TraceTuner, for its support of mixed base calling, have been used by
the research community, the private biotech sector, and the U.S. government
as components of different variant detection, genotyping and forensic
software applications (e.g. Applied Biosystems SeqScape, Paracel Genome
Assembler, MTexpert, etc.).
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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.
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This package prepares an important piece of human history to be used
with new data on new machines or to revisit older observations..