In this paper, we propose a high-throughput and energy-efficient Processing-in-Memory accelerator (PIM-Aligner) to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first reconstruct the existing sequence alignment algorithm based on BWT and FM-index such that it can be fully implemented in PIM platforms. It supports exact alignment and also handles mismatches to reduce excessive backtracking. We then develop PIM-Aligner platform that transforms SOT-MRAM array to a potential computational memory to accelerate the reconstructed alignment-in-memory algorithm incurring a low cost on top of original SOT-MRAM chips (less than 10% of chip area). Accordingly, we present a local data partitioning, mapping, and pipeline technique to maximize the parallelism in multiple computational sub-array while doing the alignment task. The simulation results show that PIM-Aligner outperforms recent platforms based on dynamic programming with ∼ 3.1× higher throughput per Watt. Besides, PIM-Aligner improves the short read alignment throughput per Watt per mm2 by ∼ 9× and 1.9× compared to FM-index-based ASIC and processing-in-ReRAM designs, respectively.