How To Install tracetuner on Debian 10
Introduction
In this tutorial we learn how to install tracetuner on Debian 10.
What is tracetuner
tracetuner is:
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..
There are three methods to install tracetuner on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install tracetuner Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install tracetuner using apt-get by running the following command:
sudo apt-get -y install tracetuner
Install tracetuner Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install tracetuner using apt by running the following command:
sudo apt -y install tracetuner
Install tracetuner Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install tracetuner using aptitude by running the following command:
sudo aptitude -y install tracetuner
How To Uninstall tracetuner on Debian 10
To uninstall only the tracetuner package we can use the following command:
sudo apt-get remove tracetuner
Uninstall tracetuner And Its Dependencies
To uninstall tracetuner and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove tracetuner
Remove tracetuner Configurations and Data
To remove tracetuner configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge tracetuner
Remove tracetuner configuration, data, and all of its dependencies
We can use the following command to remove tracetuner configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge tracetuner
Dependencies
tracetuner have the following dependencies:
References
Summary
In this tutorial we learn how to install tracetuner package on Debian 10 using different package management tools: apt, apt-get and aptitude.