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相关概念视频

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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有效的端到端长读序列映射使用minimap2-fpga与硬件加速链接集成.

Kisaru Liyanage1,2,3, Hiruna Samarakoon1,2,3, Sri Parameswaran4

  • 1School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia.

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硬件加速显著加快了长读序列的序列映射. 新的minimap2-fpga工具为牛津纳米孔技术和PacBio数据提供了显著的性能提升,精度损失最小.

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科学领域:

  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学
  • 基因组学就是基因组学.

背景情况:

  • Minimap2是第三代长读序列的基于参考的序列映射的标准.
  • 现有的软件虽然高效,但对于大规模的基因组数据集需要进一步提高速度.

研究的目的:

  • 开发和评估minimap2-fpga,使用现场可编程网关数组 (FPGA) 的硬件加速版本的minimap2.
  • 解决整合FPGA加速的挑战,包括对大型数据集的处理时间预测,数据传输和内存优化.

主要方法:

  • 集成了一个优化为链接到minimap2软件的FPGA内核.
  • 开发用于预测硬件处理时间和管理多线程环境中的开销的策略.
  • 优化内存管理,以处理大型,现实的测序数据集.

主要成果:

  • Minimap2-fpga实现了显著的加快速度:对于牛津纳米孔技术 (ONT) 来说,速度高达79%,对于太平洋生物科学 (PacBio) 数据集来说,速度高达53%,而没有基层对齐.
  • 在基层对齐的情况下,加快速度高达ONT的62%,PacBio的10%.
  • 对于数据类型和对齐模式,准确性仍然与原始的minimap2可比.

结论:

  • Minimap2-FPGA为长读序列映射提供了显著的性能提升.
  • 该解决方案兼容英特尔和Xilinx FPGA系统.
  • 为FPGA链接内核提供了一个文档库,用于未来对序列对齐软件开发的研究.