Dataset Information

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 with 105 sequences is found in ∼17 min, while the fastest alternative tool requires 10 days. CompAIRR has been integrated with the machine learning ecosystem immuneML to speed up commonly used AIRR-based machine learning applications.

Availability and implementation

CompAIRR code and documentation are available at https://github.com/uio-bmi/compairr. Docker images are available at https://hub.docker.com/r/torognes/compairr. The code to replicate the synthetic datasets, scripts for benchmarking and creating figures, and all raw data underlying the figures are available at https://github.com/uio-bmi/compairr-benchmarking.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Rognes T

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

REPOSITORIES: biostudies-literature

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Publications

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

Rognes Torbjørn T Scheffer Lonneke L Greiff Victor V Sandve Geir Kjetil GK

Bioinformatics (Oxford, England) 20220901 17

<h4>Motivation</h4>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 enab ...[more]

PMID: 35852318

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Dataset Information

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

Motivation

Results

Availability and implementation

Supplementary information

Publications

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

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