用Shasta进行分相纳米孔组装和使用GFAse进行模块化图形分相
Ryan Lorig-Roach1, Melissa Meredith2, Jean Monlong2
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; rlorigro@ucsc.edu pacarnev@ucsc.edu bpaten@ucsc.edu.
Genome research
|April 16, 2024
概括
使用长读序列的无参考基因组分期改进了牛津纳米孔技术 (ONT) 数据的新方法. 这些进展提高了理解基因组内的DNA变异和遗传的准确性.
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.
- 分子生物学分子生物学
背景情况:
- 无参考基因组分相对于分析等位基因遗传和DNA变异的表型效应至关重要.
- 长读测序和de novo组装通常用于全面的基因组分期,特别是在复杂的区域.
研究的目的:
- 开发和提出新的,具有成本效益的方法,用于准确的基因组分期的牛津纳米孔技术 (ONT) 序列数据.
- 为大规模基因组研究提高基因组分期的效率和可访问性.
主要方法:
- 利用Shasta基因组组装器对ONT序列数据进行准确的分相.
- 开发了GFAse,这是一个模块化工具,用于扩展相位连续性到染色体尺度.
- 使用新的ONT PromethION测序变体测试的方法,包括近距离结合数据.
主要成果:
- 使用描述的方法,证明了ONT数据的精确基因组分期.
- 通过更新的,更准确的ONT读数,在组装质量方面取得了显著的改进.
- 验证了Shasta组装器和GFAse工具在大规模阶段化中的有效性.
结论:
- 开发的方法为无参考基因组分期提供了更容易获得和更准确的方法.
- 在ONT测序技术的进步显著提高了基因组组装和分阶段的质量.
- 这些工具有助于更深入地了解基因组变异及其对表型的影响.
相关概念视频
01:57Sanger Sequencing
779.2K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
779.2K
03:00Next-generation Sequencing
101.7K
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....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
101.7K
03:36Genome Annotation and Assembly
22.2K
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.
22.2K
01:05Maxam-Gilbert Sequencing
13.7K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
13.7K