CompAIRR

CompAIRR performs comparative analysis of adaptive immune receptor repertoires (AIRRs) to identify overlapping and similar receptor sequences across individuals for studies of convergent immune responses.

Key Features:

• Ultra-Fast Computation: Performs exact and approximate sequence matching to compute AIRR overlap rapidly.
• Scalability: Handles large datasets to enable extensive pairwise comparisons across many AIRRs.
• Resource Efficiency: Achieves up to 1000-fold faster computation and uses one-third the memory of state-of-the-art methods; for example, it can compute exact pairwise AIRR overlap for up to 10^4 AIRRs and 10^5 sequences in approximately 17 minutes versus about 10 days on the same hardware.
• Integration with Machine Learning: Integrates with immuneML to accelerate machine-learning workflows on AIRR data.

Scientific Applications:

• Shared-sequence identification: Detects identical or similar AIR sequences across individuals to reveal convergent immune response patterns.
• Diagnostic and therapeutic development: Supports discovery of sequence-based biomarkers for diagnostics and therapeutic strategies.
• Immunogenomics studies: Enables large-scale analysis of immune repertoire diversity and specificity.

Methodology:

Employs algorithms for exact and approximate sequence matching to compute AIRR overlap between sets of repertoires.