A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level
A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level
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DOI：
10.1093/gigascience/giaa086
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发表时间：
2020-08-01
期刊：
影响因子：
9.2
通讯作者：
Perdomo, Maria F.
中科院分区：
文献类型：
--
作者：
Pratas, Diogo;Toppinen, Mari;Perdomo, Maria F.
背景资料：测序技术的进步使多种微生物和宿主基因组的表征成为可能，开辟了新的知识前沿，同时点燃了新的应用和研究前景。其中之一是调查人体内的病毒群落及其对健康和疾病的影响。为此，对来自多个组织的样本的研究至关重要，然而，这种分析的复杂性需要专用的管道。我们提供了一个自动和有效的管道，用于识别，组装和分析病毒基因组，结合来自多个器官的DNA序列数据。TRACESpipe依赖于3种模式之间的合作：基于压缩的预测，序列比对和从头组装。该管道是超快的，并提供，此外，敏感数据的安全传输和存储。调查结果：TRACESPipe在合成和离体数据集上进行测试时表现出色，识别和重建了所有病毒基因组，包括那些具有高水平单核苷酸多态性的病毒基因组。它还检测到不同器官之间的最低水平的基因组变异。结论：TRACESPipe的独特能力，同时处理和分析来自不同来源的样品，使内部主机变异性的评估。这为研究病毒的组织嗜性、进化、适应性和疾病相关性提供了可能性。此外，其他功能，如DNA损伤估计和线粒体DNA重建和分析，以及外源控制，将该管道的实用性扩展到其他领域，如法医学和古代DNA研究。TRACESPipe是在GPL v3下发布的，可在https://github.com/viromelab/tracespipe上免费下载。
Background: Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data. Findings: TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs. Conclusions: TRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.