SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures
文献类型：会议论文
| 作者 | K Xu; R Kobus; YD Chan; P Gao; XX Meng; YJ Wei; B Schmidt; WG Liu |
| 出版日期 | 2018 |
| 会议日期 | 2018 |
| 会议地点 | Eugene |
| 英文摘要 | Modern high throughput sequencing platforms can produce large amounts of short read DNA data at low cost. Error correction is an important but time-consuming initial step when processing this data in order to improve the quality of downstream analyses. In this paper, we present a Scalable Parallel Error CorrecToR designed to improve the throughput of DNA error correction for Illumina reads on various parallel platforms. Our design is based on a k-spectrum approach where a Bloom filter is frequently probed as a key operation and is optimized towards AVX-512-based multi-core CPUs, Xeon Phi many-cores (both KNC and KNL), and heterogeneous compute clusters. A number of architecture-specific optimizations are employed to achieve high performance such as memory alignment, vectorized Bloom filter probing, and a stack-based iteration to eliminate recursion. Our experiments show that our optimizations result in speedups of up to 2.8, 5.2, and 9.3 on a CPU (Xeon W-2123), a KNC-based Xeon Phi (31S1P), and a KNL-based Xeon Phi (7210), respectively, compared to a multi-threaded CPU reference implementation for the error correction stage. Furthermore, when executed on the same hardware, SPECTR achieves a speedup of up to 1.7, 2.1, 2.4, and 6.4, compared to the state-of-the-art tools Lighter, BLESS2, RECKONER, and Musket, respectively. In addition, our MPI implementation exhibits an efficiency of around 86% when executed on 32 nodes of the Tianhe-2 supercomputer. |
| 语种 | 英语 |
| 源URL | [http://ir.siat.ac.cn:8080/handle/172644/14062]  |
| 专题 | 深圳先进技术研究院_数字所 |
| 推荐引用方式 GB/T 7714 | K Xu,R Kobus,YD Chan,et al. SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures[C]. 见:. Eugene. 2018. |
入库方式： OAI收割
来源：深圳先进技术研究院
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