  The proliferation of high-throughput sequencing machines ensures rapid
generation of up to billions of short nucleotide fragments in a short period of
time. This massive amount of sequence data can quickly overwhelm today's
storage and compute infrastructure. This paper explores the use of hardware
acceleration to significantly improve the runtime of short-read alignment, a
crucial step in preprocessing sequenced genomes. We focus on the Levenshtein
distance (edit-distance) computation kernel and propose the ASAP accelerator,
which utilizes the intrinsic delay of circuits for edit-distance computation
elements as a proxy for computation. Our design is implemented on an Xilinx
Virtex 7 FPGA in an IBM POWER8 system that uses the CAPI interface for cache
coherence across the CPU and FPGA. Our design is $200\times$ faster than the
equivalent C implementation of the kernel running on the host processor and
$2.2\times$ faster for an end-to-end alignment tool for 120-150 base-pair
short-read sequences. Further the design represents a $3760\times$ improvement
over the CPU in performance/Watt terms.
