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MTBseq-nf:通过为MTBseq管道提供用户友好的Nextflow包装器,实现可扩展的结核病基因组学"大数据"分析

Abhinav Sharma¹, Davi Josué Marcon^2,3, Johannes Loubser¹

¹SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.

|December 31, 2025

概括

一个新的生物信息学工具MTBseq-nf增强了结核病全基因组测序分析. 这种Nextflow包装提供并行处理以获得更快的结果,提高基因组监测效率.

科学领域:

生物信息学是一种生物信息学.
基因组监测基因组监测
结核病菌菌菌的结核病菌的结核病菌.

背景情况:

最初的MTBseq管道 (2018) 解决了使用全基因组测序 (WGS) 结核病 (TB) 研究中的生物信息学挑战.
它是第一个 GitHub 工具,用于全面的 MTBC WGS 分析,包括质量控制,映射,变异调用,谱系分类,耐药性预测和家族遗传推断.
然而,它的线性架构限制了在高性能和云计算环境中的可扩展性.

研究的目的:

开发一个优化版本的MTBseq管道,以提高性能和可扩展性.
在结核病研究中引入并行化功能,以更快地进行WGS数据分析.
确保结核病基因组监测的可复制性和平台独立性.

主要方法:

开发MTBseq-nf,用于MTBseq管道的Nextflow包装.
对同步分析实例的并行实现.
在专用计算服务器上使用90万个结核病基因组进行基准测试.
与nf-core,Bioconda和Biocontainers的最佳实践进行集成.

主要成果:

与标准的MTBseq管道相比,MTBseq-nf表现出明显更快的执行速度.
对于超过20个样本的队列,MTBseq-nf的并行模式的速度至少是20倍.
包装保证了可重复性和平台独立性.

结论:

MTBseq-nf为结核病基因组监测提供了一个可扩展和高效的解决方案.
并行Nextflow封装克服了原来的MTBseq管道的局限性.
这一进步有助于对Mycobacterium tuberculosis WGS数据进行更快,更可靠的分析.

关键词:

最多可能的TBTseqqq 结核病菌菌菌的结核病菌的结核病菌.下一个流程下一个流程生物信息管道中的生物信息管道基因组监测对基因组进行监测.结核病的基因组学进行全基因组测序.工作流的工作流.

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相关概念视频

Next-generation Sequencing

Next-generation Sequencing

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Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....