FastZ: accelerating gapped whole genome alignment on GPUs
FastZ: accelerating gapped whole genome alignment on GPUs
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FastZ：在 GPU 上加速有缺口的全基因组比对
DOI：
10.1145/3458817.3476202
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发表时间：
2021
期刊：
影响因子：
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通讯作者：
Thottethodi, Mithuna
中科院分区：
文献类型：
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作者：
Gundabolu, Sree Charan;Vijaykumar, T. N.;Thottethodi, Mithuna
认识到全基因组比对（WGA）的重要性，美国国立卫生研究院维护LASTZ，一个连续的WGA应用程序。随着基因组数据的增长，迫切需要可扩展的高性能WGA。不幸的是，使用动态编程（DP）的高灵敏度"间隙"比对是缓慢的，而使用无间隙滤波的更快比对通常不太灵敏。FastZ采用了一种新颖的检查器-执行器方案，其中（a）除了在常见的极短的比对中，检查器执行有限的、急切的回溯以消除执行器之外，轻量级的检查器省略了DP回溯，（B）执行器修剪避免了不必要的工作。此外，FastZ采用基于寄存器的循环缓冲来大幅减少内存流量，并将DP问题按大小进行分组以实现负载平衡。FastZ在RTX 3080 GPU上运行，我们的LASTZ多核实现分别实现了111倍和20倍于顺序LASTZ的加速。
Recognizing the importance of whole genome alignment (WGA), the National Institutes for Health maintains LASTZ, a sequential WGA application. As genomic data grows, there is a compelling need for scalable, high-performance WGA. Unfortunately, high-sensitivity, `gapped' alignment which uses dynamic programming (DP) is slow, whereas faster alignment with ungapped filtering is often less sensitive. We developFastZ, a GPU-accelerated, gapped WGA software which matches gapped LASTZ in sensitivity.FastZemploys a novelinspector-executorscheme in which (a) thelightweightinspector elides DP traceback except in common, extremely short alignments, where the inspector performs limited,eagertraceback to eliminate the executor, and (b)executor trimmingavoids unnecessary work. Further,FastZemploysregister-based cyclic-bufferingto drastically reduce memory traffic, andgroups DP problems by sizefor load balance.FastZrunning on an RTX 3080 GPU and our multicore implementation of LASTZ achieve 111x and 20x speedups over the sequential LASTZ, respectively.