Rapidly developing Next Generation Sequencing technologies produce huge amounts of short reads that consisting randomly fragmented DNA base pair strings. Assembling of those short reads poses a challenge on the mapping of reads to a reference genome in terms of both sensitivity and execution time. In this paper, we propose a customized many-core hardware acceleration platform for short read mapping problems based on hash-index method. The processing core is highly customized to suite both 2-hit string matching and banded Smith-Waterman sequence alignment operations, while distributed memory interface with 3D-stacked architecture provides high bandwidth and low access latency for highly customized dataset partitioning and memory access scheduling. Conformal with original BFAST program, our design provides an amazingly 45,012 times speedup over software approach for single-end short reads and 21,102 times for paired-end short reads, while also beats similar single FPGA solution for 1466 times in case of single end reads. Optimized seed generation gives much better sensitivity while the performance boost is still impressive.