MultiPrime: A Reliable and Efficient Tool for Targeted Next-Generation Sequencing

Abstract We present multiPrime, a novel tool that automatically designs minimal primer sets for target next generation sequencing. It enhances coverage by designing primers with mismatch tolerance, ensuring high compatibility and specificity. We compared the performance of multiPrime to that of conventional tools using a dataset of 43,016 sequences from eight viruses. Our results demonstrate that multiPrime outperformed the conventional tools and that the multiPrime-designed primer set successfully amplified the target amplicons. Furthermore, we expanded the application of multiPrime to include thirty viruses and validated the efficacy of multiPrime-designed primers in eighty clinical specimens. The results indicated a sensitivity of 94% and specificity of 89%.