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基于容器的可扩展和多功能管道,用于新的基因组组装和细菌注释

Felipe Marques de Almeida^1,2, Tatiana Amabile de Campos^2,3, Georgios Joannis Pappas^1,2

¹Programa de Pós-graduação em Biologia Molecular, Universidade de Brasilia, Brasília, FD, 70910-900, Brazil.

|November 16, 2023

概括

新的Nextflow管道通过整合质量控制,新组装和全面的基因组注释来简化细菌基因组学,以加速研究. 这些工具为所有技能水平的研究人员增强了细菌基因组分析.

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:

DNA 测序的进步使得细菌染色体组件能够更快,更具成本效益.
将原始测序阅读转换为完整的基因组模型,带来了计算方面的挑战.
基于容器的Nextflow管道通过可适应的策略来应对这些挑战.

研究的目的:

开发用户友好,可定制的细菌基因组分析管道.
整合质量控制,新组装和全面的基因组注释.
为了为新手和专家用户提供常规的细菌基因组学研究.

主要方法:

使用Nextflow开发基于容器的管道.
管道包括用于质量控制,新基因组组装和细菌基因组注释的模块.
标注管道提供标准基因预测,功能推断和临床应用相关的预测 (病毒性,耐药性等). ) 的情况.

主要成果:

管道提供基于序列数据类型的可适应处理策略.
注释管道包括对毒性因子,抗生素耐药性基因,二次代谢产物,菌体和等离子体的预测.
结果可以通过报告,基因组浏览器和交互式Web应用程序访问.

结论:

用户友好的管道通过集成的计算工具简化了细菌基因组学研究.
这些管道促进了细菌基因组的常规分析和探索.
使用来自临床Klebsiella pneumoniae样本的测序数据证明了有效性.

关键词:

抗生素耐药性抗生素耐药性细菌基因组学是一种细菌基因组学.下一个流是下一个流.管道管道管道是指管道的管道.公共卫生公共卫生.毒性毒性是一种毒性.

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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...