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Computational tool choice impacts CRISPR spacer-protospacer detection.

Uri Neri·Antonio Pedro Camargo·Brian Bushnell·Rick Beeloo·Simon Roux
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Abstract

MOTIVATION: CRISPR spacer-protospacer matching is widely used to infer host-virus interactions in microbial and viromics studies, but the choice of sequence search or alignment tool and its reporting behavior is often under-evaluated for this specific task. RESULTS: Using synthetic, semi-synthetic, and real datasets, we benchmarked commonly used tools and observed substantial differences in recall, runtime, and resource usage across distance metrics and thresholds. Our analyses support practical defaults for large-scale spacer-target matching and clarify trade-offs between exhaustive and heuristic approaches. AVAILABILITY: Source code and benchmark workflows are available at https://github.com/UriNeri/spacer_matching_bench. Data and run artifacts are archived on Zenodo (https://doi.org/10.5281/zenodo.15171878).

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Uri Neri, Antonio Pedro Camargo, Brian Bushnell, Rick Beeloo, Simon Roux. 2026-07-02. Computational tool choice impacts CRISPR spacer-protospacer detection.. https://doi.org/10.1093/bioinformatics%2Fbtag394

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