Computational Tool Choice Impacts CRISPR Spacer-Proto spacer Detection.
basic_science · Level V
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- Record sourced from PubMed, PMID 42371756.
- Also identified by DOI 10.1093/bioinformatics/btag394.
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Abstract
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. 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. 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 data are available at Bioinformatics online.