Fig. 1

ClonoCalc and ClonoPlot provide a GUI to guide the scientist through a complete workflow for generating publication-ready figures from NGS raw data: a Animal and human TCR and IG sequences are input, ClonoCalc pre-processes FASTQ files. ClonoPlot creates final plots using R scripts for data comparison and visualization. b Screenshots from ClonoCalc application. From the start screen, a button opens a file dialog, where FASTQ-files can be chosen. Parameters for sub-tasks of data preprocessing can be chosen from buttons depicted on the right. A log file to review the analysis will be generated automatically and made available on the finish screen. c ClonoPlot’s user interface (i) is divided into two sides: on the left, folders can be chosen from the working directory and will be added to the treeview. On the right, various functions can be selected, each of which produces a plot. Examples of resulting plots include frequency plots (ii), circular visualization of similarities between samples (iii), and CDR3 intersection plots including Venn diagrams and heatmaps (iV and V)