Name
Title | ||
|---|---|---|
Spectr: Scalable Parallel Short Read Error Correction On Multi-Core And Many-Core Architectures |
Abstract | ||
|---|---|---|
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. SPECTR is available at https://github.com/Xu-Kai/SPECTR. |
Year | DOI | Venue |
|---|---|---|
2018 | 10.1145/3225058.3225060 | PROCEEDINGS OF THE 47TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING |
Keywords | Field | DocType |
Bioinformatics, Xeon Phi, Vectorization, MPI, Bloom filter | Bloom filter,Supercomputer,Xeon Phi,Computer science,Parallel computing,Error detection and correction,Xeon,Multi-core processor,Speedup,Data structure alignment | Conference |
ISSN | Citations | PageRank |
0190-3918 | 0 | 0.34 |
References | Authors | |
25 | 8 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Kai Xu | 1 | 56 | 20.13 |
| Robin Kobus | 2 | 1 | 2.05 |
| Yuandong Chan | 3 | 23 | 3.90 |
| Ping Gao | 4 | 0 | 0.34 |
| Xiangxu Meng | 5 | 6 | 4.89 |
| Yanjie Wei | 6 | 17 | 2.48 |
| Bertil Schmidt | 7 | 19 | 12.95 |
| Weiguo Liu | 8 | 339 | 28.23 |