通过Nextflow和nf-core赋权生物信息学社区
Björn E Langer1, Andreia Amaral2,3, Marie-Odile Baudement4
1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
Genome biology
|July 30, 2025
概括
使用Nextflow DSL2的nf-core框架通过促进FAIR数据原则和协作来增强生物信息学研究. 它提供了一个模块化图书馆,支持社区标准和采用,如农场动物研究联盟所见.
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
- 数据科学数据科学数据科学
背景情况:
- 标准化分析管道对于生物信息学研究中的FAIR数据原则 (可查找性,可访问性,互操作性,可重复使用性) 是至关重要的.
- 像Nextflow和Snakemake这样的命令行工具正在获得引力,补充了像Galaxy这样的图形平台.
- 该nf-core框架旨在标准化生物信息学工作流程.
研究的目的:
- 报告nf-core框架的最新发展,特别是采用Nextflow DSL2.
- 突出NF-core广泛的模块和子工作流图书馆的实用性.
- 展示NF-core在研究界的采用和影响,特别是在养殖动物研究中.
主要方法:
- 在nf-core框架内开发和实施Nextflow DSL2.
- 创建一个可重复使用的模块和子工作流的全面库.
- 案例研究表明研究联盟采用了nf-core.
主要成果:
- nf-core框架现在支持Nextflow DSL2,增强工作流程开发.
- 广泛的模块和子工作流图书馆有助于逐步采用共同标准.
- nf-core已经成功地被六个EuroFAANG养殖动物研究联盟采用.
结论:
- 与Nextflow DSL2一起的nf-core框架有效地支持FAIR数据原则和生物信息学领域的合作.
- 它的模块化设计和广泛的图书馆使研究社区能够采用标准化的实践.
- nf-core的采用在像EuroFAANG这样的大规模研究倡议中证明了它的价值.
相关概念视频
03:00Next-generation Sequencing
92.6K
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....
92.6K
01:23Flow Cytometry
13.7K
The development of flow cytometry techniques began in 1934 with initial attempts by Andrew Moldavan, a bacteriologist who counted the cells in a flowing capillary system. Moldavan pumped cells through a capillary tube focused under a microscope for visualization. The invention of photometry allowed the measurement of differentially-stained cells, and Louis Kamentsky developed the first multiparameter flow cytometer in 1965 to identify and count the cancer cells in cervical tissue specimens.
In...
In...
13.7K
02:55Synthetic Biology
5.0K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
5.0K
02:02Genomics
37.5K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
37.5K
01:17Flow Sheet
1.9K
Flowsheets are valuable tools in nursing documentation. They enable healthcare professionals to efficiently record and monitor various patient assessments and measurements in a consolidated format.
Here's a closer look at the examples of flowsheets commonly used by nurses:
Graphic Sheet Documentation:
Here's a closer look at the examples of flowsheets commonly used by nurses:
Graphic Sheet Documentation:
1.9K
01:24Tagging and Fusion Proteins
6.9K
Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
6.9K