This repository contains the source code of the paper "Accelerating Long Read Alignment on Three Processors", by Zonghao Feng, Shuang Qiu, Lipeng Wang, and Qiong Luo.
Evaluation of the base-level alignment kernel. Run make to compile the following executables:
ksw_{sse2, sse41, avx2, avx512}: The original kernel in minimap2.
cpu_{sse2, sse41, avx2, avx512}: CPU version of the optimized kernel.
knl: KNL (Intel Xeon Phi processor) version.
gpu: GPU version. Variants: single block / multiple blocks with cooperative groups, global memory / shared memory (applicable to small data), score only / complete path
Evaluation of end-to-end runtime. Run make to compile. To use the MCDRAM on KNL, add numactl -m 1 before the run command.
This project is based on minimap2 (version 2.16).