Quarc - Quality Analysis and Read Control
This package contains a couple of useful programs to analyse a set of short read data.
- bin/quarc/BaseCalls.class: A program that outputs the single base calls in a data set.
Optionally, frequencies of k-mers can be analysed and the progression of average
quality scores along the reads. Run the program without parameters for further details:
java -cp bin quarc.BaseCalls
The sources can be found in src/BaseCalls.java
- bin/KL.class: This program analyses the Kullback-Leibler divergence in a given read set.
Run the program without parameters for a list of options:
java -cp bin quarc.KL
The sources can be found in src/KL.java
- generateBasecallPlot.sh: This is a shell script that uses the BaseCalls program above and
the plotting scripts in plottingScripts/generateBasecallPlot.r (and generateQualityPlot.r).
The machine has to have R and the ggplot2 library installed for the script to run.
Run the script without parameters to check the usage:
- generateKLplot.sh: This bash script runs the KL java program and then plots the results in
Gnuplot using plottingScripts/plotKLdivergence.sh. It is relying on Gnuplot being installed
in a recent enough version (requiring pm3d). Check the usage by running without parameters:
- plottingScripts/generateBasecallPlot.r / plottingScripts/generateQualityPlot.r: R scripts to plot
the results of the according java programs. Both rely on R and the ggplot2 library.
- plottingScripts/plotKLdivergence.sh: a bash script to run Gnuplot and plot the results from
the KL java program.
Try running the top level bash scripts to obtain some statistics about the data and the according
plots. If all required programs are installed, the scripts should run without any complication.
Feel free to modify the programs and scripts to satisfy your needs.
If you have any questions about the programs and how to run them, please feel free to contact me:
Jan Schroeder <firstname.lastname@example.org>