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在复杂的真核基因组和元基因组上对11个新的HiFi组装器进行了全面评估

Wenjuan Yu¹, Haohui Luo¹, Jinbao Yang^1,2

¹Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.

Genome research

|March 1, 2024

概括

这项研究对太平洋生物科学HiFi测序数据的11个de novo汇编器进行了基准测试. 建议使用hifiasm和hifiasm-meta来组装真核生物基因组和元基因组.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
计算生物学计算生物学

背景情况:

太平洋生物科学 (PacBio) 的HiFi测序提供了长时间读取 (>10 kbp) 的高精度 (<0.01%的误差).
为 HiFi 读取存在众多 de novo 组装工具,但缺乏全面的性能评估.

研究的目的:

为了全面评估11个de novo组装器对HiFi测序数据的性能.
使用HiFi阅读来识别最适合真核基因组和元基因组的组装器.

主要方法:

使用真实和合成真核细胞基因组数据集 (n=37) 和元基因组数据集 (n=6) 评估了11个de novo组装器.
使用 QUAST 和 BUSCO 评估汇编器性能,以及完成率,运行时间和内存使用等指标.

主要成果:

Hifiasm和hifiasm-meta表现出优越的性能,可以使用HiFi数据组装真核生物基因组和元基因组.
基于 ploidy,覆盖率和异构性等数据特征,组装器的性能各不相同.

结论:

建议Hifiasm和hifiasm-meta作为HiFi基基因组和元基因组组件的主要选择.
这项基准测试研究有助于研究人员选择合适的汇编器,并突出了算法改进的领域.

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相关概念视频

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

RNA-seq

RNA-seq

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...