CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching.

ABSTRACT:

Motivation

Adaptive immune receptor (AIR) repertoires (AIRRs) record past immune encounters with exquisite specificity. Therefore, identifying identical or similar AIR sequences across individuals is a key step in AIRR analysis for revealing convergent immune response patterns that may be exploited for diagnostics and therapy. Existing methods for quantifying AIRR overlap scale poorly with increasing dataset numbers and sizes. To address this limitation, we developed CompAIRR, which enables ultra-fast computation of AIRR overlap, based on either exact or approximate sequence matching.

Results

CompAIRR improves computational speed 1000-fold relative to the state of the art and uses only one-third of the memory: on the same machine, the exact pairwise AIRR overlap of 104 AIRRs

SUBMITTER: Rognes T 

PROVIDER: S-EPMC9438946 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature