Sequence alignment method and system for next-generation sequencing data based on many-core platform

The invention discloses a sequence alignment method and system for next-generation sequencing data based on a many-core platform, and the method comprises the steps: adaptively adjusting the size of aread-in data block according to the calculation capability of the platform, and achieving the mutual...

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Bibliographic Details
Main Authors ZHANG JINXIAO, YIN ZEKUN, LIU WEIGUO, LIU MEIYANG, ZHANG WEN
Format Patent
LanguageChinese
English
Published 24.07.2020
Subjects
CALCULATING
COMPUTING
COUNTING
ELECTRIC DIGITAL DATA PROCESSING
INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS
PHYSICS
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Summary:The invention discloses a sequence alignment method and system for next-generation sequencing data based on a many-core platform, and the method comprises the steps: adaptively adjusting the size of aread-in data block according to the calculation capability of the platform, and achieving the mutual covering of calculation and I/O; reducing memory overhead by utilizing a pre-allocation strategy and a lightweight memory allocation strategy based on a memory pool strategy; fully utilizing a vector processing unit of a processor, and adopting an instruction set for vectorizing and parallelizingthe calculation process. For a BWA-MEM algorithm, the overall performance of the method is remarkably improved, and the overall performance of a program achieves 3.62 times of the acceleration ratio;the algorithm thread expansibility is obviously improved; compared with the original algorithm, the core calculation part has the advantage that the acceleration ratio obtained under data sets with different sizes is 8.4-12.6.
Bibliography:Application Number: CN202010213357