checkbcphd

interpretation of DNA Sanger sequencing data

Install

All systems
curl cmd.cat/checkbcphd.sh
Debian Debian
apt-get install tracetuner
Ubuntu
apt-get install tracetuner
image/svg+xml Kali Linux
apt-get install tracetuner
Windows (WSL2)
sudo apt-get update sudo apt-get install tracetuner
Dockerfile
dockerfile.run/checkbcphd

tracetuner

interpretation of DNA Sanger sequencing data

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. 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. 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. 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.). 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. This package prepares an important piece of human history to be used with new data on new machines or to revisit older observations..