High-flux transcriptome sequencing data quality control method based on multi-core CPU (Central Processing Unit) hardware

A transcriptome sequencing and data quality technology, applied in the field of bioinformatics, can solve the problem that the computing system cannot efficiently meet the quality control of high-throughput transcriptome sequencing data, so as to overcome the bottleneck of computing efficiency, improve efficiency, and improve accuracy and speed effect

Active Publication Date: 2015-11-25
QINGDAO INST OF BIOENERGY & BIOPROCESS TECH CHINESE ACADEMY OF SCI
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Problems solved by technology

[0004] In order to solve the problem that traditional analysis methods and computing systems cannot comprehensively, accurately and efficiently meet the quality control requirements of high-throughput transcriptome sequencing data, the

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  • High-flux transcriptome sequencing data quality control method based on multi-core CPU (Central Processing Unit) hardware
  • High-flux transcriptome sequencing data quality control method based on multi-core CPU (Central Processing Unit) hardware
  • High-flux transcriptome sequencing data quality control method based on multi-core CPU (Central Processing Unit) hardware

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Embodiment Construction

[0034] The present invention will be further described in detail below in conjunction with the accompanying drawings and embodiments.

[0035] The technical scheme adopted by the invention is a multi-core CPU computer and an efficient and unified software platform built on it. Its characteristics are (1) a high-performance parallel computing and storage hardware system; (2) a comprehensive, high-performance, unified, and configurable parallel software platform.

[0036] (1) High-performance parallel computing and storage hardware

[0037] The hardware system uses multi-channel multi-core CPU for large-scale parallel computing. figure 1 It is the system structure diagram of the computing server:

[0038] First of all, multi-channel multi-core CPU parallelizes calculations, using 4-way processors, and using QPI bus connections between processors. Each processor has 8 independent computing cores, equipped with three-channel DDR3RDIMM memory, and also adapts to the computing re...

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Abstract

The present invention provides a high-flux transcriptome sequencing data quality control method based on multi-core CPU hardware. The method comprises: performing parallel processing on high-flux transcriptome sequencing data by using a multi-core CPU, so as to obtain data without low sequencing quality sequences; performing prediction and removal on rRNA sequences in the data without the low sequencing quality sequences by using the multi-core CPU, and performing qualitative identification on polluted sequences; and performing statistics and evaluation on a sequence comparison result. According to the high-flux transcriptome sequencing data quality control method based on the multi-core CPU hardware, provided by the present invention, based on a multi-core CPU computer, a computing efficiency bottleneck based on a single-core CPU hardware computer is overcome, so that high-flux transcriptome data quality control efficiency is increased by over 7 times; and by applying the high-flux transcriptome sequencing data quality control method, the accuracy and speed of the high-flux transcriptome data quality control are significantly improved, and rapid development of relevant researches of transcriptome sequencing is widely facilitated.

Description

technical field [0001] The patent of the present invention relates to bioinformatics, specifically a method for quality control of high-throughput transcriptome sequencing data based on multi-core CPU hardware, which can quickly perform quality control on high-throughput transcriptome sequencing data. Background technique [0002] High-throughput sequencing technology, also known as "next generation" sequencing technology, is a revolutionary change to traditional sequencing. It can sequence hundreds of thousands to millions of DNA / RNA molecules at a time, and has been more and more widely used. in biological research. Compared with traditional Sanger sequencing technology, the throughput of next-generation sequencing technology has increased by one to two orders of magnitude, and the amount of data is larger (100MB to several G). Transcriptome sequencing is an in-depth application based on high-throughput sequencing technology, which can conduct detailed, in-depth and compr...

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Application Information

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IPC IPC(8): G06F19/18
Inventor 周茜宁康苏晓泉徐健
Owner QINGDAO INST OF BIOENERGY & BIOPROCESS TECH CHINESE ACADEMY OF SCI
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