zkConsensus: A Zero Knowledge Proof Implementation for Consensus Sequence Generation

Abstract

Consensus sequences are reconstructed representations of original DNA strands, generated by aligning and combining multiple fragmented reads. This paper presents zkConsensus, a privacy-preserving system that verifies the generation of consensus sequences without revealing sensitive genetic information with the use of Zero-Knowledge Proofs (ZKPs). Implemented in Circom language, the circuit validates three validation parts: the consistency between original and aligned reads, the correctness of alignment scores across all read pairs, and the support for the consensus bases through majority voting. The system takes as public inputs the original reads, their lengths, and an expected score, while treating the alignments, reverse complement indications, start positions, and final consensus as private.