0000000000885261
AUTHOR
Xiangxu Meng
showing 2 related works from this author
SWMapper: Scalable Read Mapper on SunWay TaihuLight
2020
With the rapid development of next-generation sequencing (NGS) technologies, high throughput sequencing platforms continuously produce large amounts of short read DNA data at low cost. Read mapping is a performance-critical task, being one of the first stages required for many different types of NGS analysis pipelines. We present SWMapper — a scalable and efficient read mapper for the Sunway TaihuLight supercomputer. A number of optimization techniques are proposed to achieve high performance on its heterogeneous architecture which are centered around a memory-efficient succinct hash index data structure including seed filtration, duplicate removal, dynamic scheduling, asynchronous data tra…
SPECTR
2018
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 opt…