tripr

tripr analyzes IMGT/HighV-Quest output to characterize T-cell receptor (TR) and B-cell receptor immunoglobulin (BcR IG) gene rearrangements, CDR3 nucleotide and amino acid composition, clonality, and somatic hypermutation from next-generation sequencing (NGS) immunoprofiling.

Key Features:

• Detailed Gene Rearrangement Analysis: Examines V, D, and J gene usage for TR and BcR IG rearrangements.
• CDR3 Composition Analysis: Reports CDR3 amino acid and nucleotide sequences and composition.
• Clonality Assessment: Quantifies clonal diversity and detects clonal expansions in TCR and BCR repertoires.
• Somatic Hypermutation Characterization: Identifies and characterizes somatic hypermutations in BcR IG genes relevant to affinity maturation.
• Data Processing Efficiency: Benchmarked on synthetic datasets (250k–1M sequences) with a linear processing time of approximately six hours for one million sequences through the BcR IG pipeline.
• Reproducibility and Accuracy: Compared against previous Galaxy-platform pipelines, showing reproducibility and a slightly stricter preselection that filters ~0.1% more rearrangements without affecting final results.
• Comprehensive Analytical Services: Implements data wrangling, cleaning, analysis, and visualization functions for antigen receptor sequence data.

Scientific Applications:

• Immunotherapy Development: Characterizing clonality and somatic hypermutations to inform targeted immunotherapies.
• Disease Diagnosis and Monitoring: Detecting monoclonal expansions and repertoire changes for diagnoses such as lymphomas and for monitoring treatment response.
• Vaccine Research: Profiling antigen receptor diversity and specificity to support vaccine design and efficacy studies.

Methodology:

Processes IMGT/HighV-Quest output through a series of interoperable modules and performs data wrangling, cleaning, analysis, and visualization; evaluated on synthetic datasets (250k–1M sequences) and compared to Galaxy-platform pipelines.