ClonoCalc

ClonoCalc processes next-generation sequencing (NGS) data to determine T cell receptor (TCR) and B cell receptor (BCR) clonotypes and produce repertoire-level analyses.

Key Features:

• Integrated analysis pipeline: Complete pipeline for TCR and BCR clonotype determination from raw NGS data in human and animal samples.
• Demultiplexing and preprocessing: Demultiplexer for barcode splitting and preprocessing of raw sequencing reads.
• MiXCR-based sequence extraction: Uses MiXCR to merge paired-end reads and extract TCR and BCR sequences.
• ClonoPlot visualization: Wraps the R package tcR and provides custom plots for descriptive and comparative repertoire analyses, including diversity and distribution metrics.
• Implementation and modularity: Implemented in Java and R with a modular architecture separating preprocessing, sequence extraction, and visualization components.

Scientific Applications:

• Immune repertoire profiling: Analysis of TCR and BCR diversity and clonotype distributions to study immune status in health and disease.
• Immunology research: Comparative investigations of adaptive immune responses using repertoire metrics.
• Veterinary science: Application to human and animal samples for cross-species repertoire analyses.
• Translational medicine and vaccine development: Use of repertoire dynamics to inform vaccine responses and translational studies.
• Autoimmunity studies: Characterization of repertoire changes related to autoimmune conditions.

Methodology:

Demultiplexing via a barcode-splitting demultiplexer, MiXCR for merging paired-end reads and extracting TCR/BCR sequences, and ClonoPlot wrapping the R package tcR for visualization; implemented in Java and R.