tripr

tripr analyzes antigen receptor sequences from NGS immunoprofiling to characterize V(D)J gene usage, CDR3 composition, clonality, and somatic hypermutation in TR and BcR IG repertoires.

Key Features:

• Integration with IMGT/HighV-Quest: Processes output files from IMGT/HighV-Quest for downstream immunoprofiling analyses.
• Interoperable modules: Provides modules that quantify V, D, and J gene usage and report CDR3 composition at both amino acid and nucleotide levels.
• Clonality analysis: Assesses clonality of T cell receptors (TR) and B cell receptor immunoglobulins (BcR IG).
• Somatic hypermutation characterization: Identifies and characterizes somatic hypermutations within BcR IG genes.
• Performance and scalability: Demonstrated capacity to process large synthetic datasets with linear response time across 250k–1M sequences.

Scientific Applications:

• Immune repertoire profiling: Characterizes repertoire diversity and V(D)J usage from NGS antigen receptor sequence data.
• Clonal expansion analysis: Detects and quantifies clonal expansions in T and B cell repertoires.
• Somatic hypermutation studies: Maps somatic hypermutations in BcR IG to study affinity maturation and evolution.
• Method comparison and reproducibility: Supports reproducibility assessments and comparisons against previous pipelines (e.g., Galaxy).

Methodology:

Processes IMGT/HighV-Quest output; uses interoperable modules to compute V, D, J gene usage and CDR3 composition at amino acid and nucleotide levels; performance evaluated on synthetic datasets (250k–1M sequences) with linear scaling and approximately six hours for one million sequences through the full BcR IG pipeline; reproducibility tested against prior Galaxy-based pipelines.