AutoFFinder: A reconfigurable hardware-accelerated platform for multi-guide CRISPR/Cas9 off-target search.

AutoFFinder finds CRISPR/Cas9 off-target sites for 128 gRNAs on the human reference genome (hg38) at edit-distance threshold 6 in 68.43 seconds.

• Why it matters: Safety-focused genome editing needs genome-wide off-target site identification, but existing approaches slow down sharply with many gRNAs and higher edit-distance thresholds.
• What they did: The platform uses a runtime-reconfigurable FPGA overlay (ReLev) to stream genomic data and evaluate up to 128 gRNAs concurrently, then a parallel CPU stage reconstructs exact alignments under mismatch and bulge constraints.
• The result: For 128 gRNAs at threshold 6, it completes end-to-end search in 68.43 seconds versus 190.62 seconds on a GPU Myers’ Bitparallel method and 38.0–38.7 minutes on CPU methods, while completeness validation shows it recovers all potential OTSs.

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