Over the past decade, mtDNA-Server established itself as one of the most widely used variant calling web-services for human mitochondrial genomes. The service accepts sequencing data in BAM format and returns an annotated variant analysis report for both homoplasmic and heteroplasmic variants. In this work we present mtDNA-Server 2, which includes several new features highly requested by the community. Most importantly, it includes (a) the integration of a novel variant calling mode that accurately call insertions, deletions and single nucleotide variants at once, (b) the integration of additional quality control and input validation modules, (c) a method to estimate the required coverage to minimize false positives and (d) an interactive analytics dashboard. Furthermore, we migrated the complete analysis workflow to the Nextflow workflow manager for improved parallelization, reproducibility and local execution. Recognizing the importance of insertions and deletions as well as offering novel quality control, validation and reporting features, mtDNA-Server 2 provides researchers and clinicians a new state-of-the-art analysis platform for interpreting mitochondrial genomes. mtDNA-Server 2 is available via mitoverse, our analysis platform that offers a centralized place for mtDNA analysis in the cloud. The web-service, source code and its documentation are freely accessible at https://mitoverse.i-med.ac.at.

中文翻译：

---

mtDNA-Server 2：通过高度并行的数据处理和交互式分析推进线粒体 DNA 分析

在过去的十年中，mtDNA-Server 已成为人类线粒体基因组使用最广泛的变异调用网络服务之一。该服务接受 BAM 格式的测序数据，并返回同质和异质变体的带注释的变体分析报告。在这项工作中，我们展示了 mtDNA-Server 2，其中包括社区强烈要求的几个新功能。最重要的是，它包括（a）集成一种新的变异识别模式，可以一次准确地识别插入、缺失和单核苷酸变异，（b）附加质量控制和输入验证模块的集成，（c）一种估计方法最大限度地减少误报所需的覆盖范围和 (d) 交互式分析仪表板。此外，我们将完整的分析工作流程迁移到 Nextflow 工作流程管理器，以改进并行性、再现性和本地执行。认识到插入和删除的重要性以及提供新颖的质量控制、验证和报告功能，mtDNA-Server 2 为研究人员和临床医生提供了一个用于解释线粒体基因组的新的最先进的分析平台。 mtDNA-Server 2 可通过 mitoverse 获得，mitoverse 是我们的分析平台，为云中的 mtDNA 分析提供集中位置。网络服务、源代码及其文档可在 https://mitoverse.i-med.ac.at 上免费访问。