Fast and accurate DNASeq variant calling workflow composed of LUSH toolkit.

IF 3.8 3区 医学 Q2 GENETICS & HEREDITY Human Genomics Pub Date : 2024-10-10 DOI:10.1186/s40246-024-00666-w
Taifu Wang, Youjin Zhang, Haoling Wang, Qiwen Zheng, Jiaobo Yang, Tiefeng Zhang, Geng Sun, Weicong Liu, Longhui Yin, Xinqiu He, Rui You, Chu Wang, Zhencheng Liu, Zhijian Liu, Jin'an Wang, Xiangqian Jin, Zengquan He
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Abstract

Background: Whole genome sequencing (WGS) is becoming increasingly prevalent for molecular diagnosis, staging and prognosis because of its declining costs and the ability to detect nearly all genes associated with a patient's disease. The currently widely accepted variant calling pipeline, GATK, is limited in terms of its computational speed and efficiency, which cannot meet the growing analysis needs.

Results: Here, we propose a fast and accurate DNASeq variant calling workflow that is purely composed of tools from LUSH toolkit. The precision and recall measurements indicate that both the LUSH and GATK pipelines exhibit high levels of consistency, with precision and recall rates exceeding 99% on the 30x NA12878 dataset. In terms of processing speed, the LUSH pipeline outperforms the GATK pipeline, completing 30x WGS data analysis in just 1.6 h, which is approximately 17 times faster than GATK. Notably, the LUSH_HC tool completes the processing from BAM to VCF in just 12 min, which is around 76 times faster than GATK.

Conclusion: These findings suggest that the LUSH pipeline is a highly promising alternative to the GATK pipeline for WGS data analysis, with the potential to significantly improve bedside analysis of acutely ill patients, large-scale cohort data analysis, and high-throughput variant calling in crop breeding programs. Furthermore, the LUSH pipeline is highly scalable and easily deployable, allowing it to be readily applied to various scenarios such as clinical diagnosis and genomic research.

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快速准确的 DNASeq 变异调用工作流程由 LUSH 工具包组成。
背景:全基因组测序(WGS)在分子诊断、分期和预后方面的应用越来越普遍,因为它的成本不断降低,而且几乎能检测到与患者疾病相关的所有基因。目前广为接受的变异调用管道 GATK 在计算速度和效率方面存在局限性,无法满足日益增长的分析需求:在此,我们提出了一种快速、准确的 DNASeq 变异调用工作流程,该流程完全由 LUSH 工具包中的工具组成。精确度和召回率的测量结果表明,LUSH 和 GATK 管道都表现出了高度的一致性,在 30x NA12878 数据集上的精确度和召回率都超过了 99%。在处理速度方面,LUSH 管道优于 GATK 管道,仅用 1.6 小时就完成了 30 倍 WGS 数据分析,比 GATK 快约 17 倍。值得注意的是,LUSH_HC 工具仅用 12 分钟就完成了从 BAM 到 VCF 的处理,比 GATK 快约 76 倍:这些发现表明,在 WGS 数据分析方面,LUSH 管道是 GATK 管道的一个非常有前途的替代方案,有望显著改善急性病患者的床边分析、大规模队列数据分析以及作物育种项目中的高通量变异调用。此外,LUSH 管道具有高度可扩展性,易于部署,可随时应用于临床诊断和基因组研究等各种场景。
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来源期刊
Human Genomics
Human Genomics GENETICS & HEREDITY-
CiteScore
6.00
自引率
2.20%
发文量
55
审稿时长
11 weeks
期刊介绍: Human Genomics is a peer-reviewed, open access, online journal that focuses on the application of genomic analysis in all aspects of human health and disease, as well as genomic analysis of drug efficacy and safety, and comparative genomics. Topics covered by the journal include, but are not limited to: pharmacogenomics, genome-wide association studies, genome-wide sequencing, exome sequencing, next-generation deep-sequencing, functional genomics, epigenomics, translational genomics, expression profiling, proteomics, bioinformatics, animal models, statistical genetics, genetic epidemiology, human population genetics and comparative genomics.
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