Computational Tool Choice Impacts CRISPR Spacer-Proto spacer Detection

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). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.