CIEVaD:用于快速按需部署基因组变异检测端到端测试的轻量级工作流程集

Viruses Pub Date : 2024-09-11 DOI:10.3390/v16091444
Thomas Krannich, Dimitri Ternovoj, Sofia Paraskevopoulou, Stephan Fuchs
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引用次数: 0

摘要

在基因组测序时代,鉴定基因组变异已成为一项常规工作。尤其是单个或几个核苷酸的小基因组变异,人们经常研究它们对生物表型的影响。因此,在许多生物应用中,精确、稳健地检测变体的确切基因组位置和核苷酸组成的变化至关重要。虽然变异检测的许多关键步骤都有大量的方法,但彻底测试检测过程和评估其结果仍然是一个繁琐的过程。在这项工作中,我们提出了一系列易于应用和高度可修改的工作流程,以促进合成测试数据的生成,并评估用户提供的变体集与测试数据的一致性。这些工作流程是在 Nextflow 中实现的,并且在 GPL-3.0 许可下开源,可在 Github 上免费获取。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
CIEVaD: A Lightweight Workflow Collection for the Rapid and On-Demand Deployment of End-to-End Testing for Genomic Variant Detection
The identification of genomic variants has become a routine task in the age of genome sequencing. In particular, small genomic variants of a single or few nucleotides are routinely investigated for their impact on an organism’s phenotype. Hence, the precise and robust detection of the variants’ exact genomic locations and changes in nucleotide composition is vital in many biological applications. Although a plethora of methods exist for the many key steps of variant detection, thoroughly testing the detection process and evaluating its results is still a cumbersome procedure. In this work, we present a collection of easy-to-apply and highly modifiable workflows to facilitate the generation of synthetic test data, as well as to evaluate the accordance of a user-provided set of variants with the test data. The workflows are implemented in Nextflow and are open-source and freely available on Github under the GPL-3.0 license.
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