Bioinformatics Bachelor of Health Sciences Program.
Department of Pediatrics, Cardiac Sciences, Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, Libin Cardiovascular Institute of Alberta.
Bioinformatics. 2017 Aug 15;33(16):2573-2574. doi: 10.1093/bioinformatics/btx202.
In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome. EzMap combines a number of tools to clean, filter, and subtract WGS reads by mapping to a reference human assembly. The relative abundance of each virus present is estimated using a maximum likelihood approach that accounts for genome size, and results are presented with interactive visualizations and taxonomy-based summaries that enable rapid insights. The pipeline is automated to run on both workstations and computing clusters for all steps. EzMap automates an otherwise tedious and time-consuming protocol and aims to facilitate rapid and reproducible insights from cfDNA.
EzMap is freely available at https://github.com/dekoning-lab/ezmap.
Supplementary data are available at Bioinformatics online.
在实体器官移植受者中，必须在免疫抑制和免疫能力之间达到微妙的平衡，这在实时监测中很难实现。最近有人提出，通过分析人类病毒组的状况，对无细胞 DNA（cfDNA）进行鸟枪法测序是一种间接评估移植受者免疫功能的新方法。为了促进探索人类病毒组作为免疫状态指标的效用，并使临床医生能够快速、直接地进行分析，我们开发了一种完全自动化的计算管道 EzMap，用于对人类病毒组进行宏基因组分析。EzMap 结合了多种工具，通过映射到参考人类基因组来清洁、过滤和减去 WGS 读数。使用最大似然法估计每种病毒的相对丰度，该方法考虑了基因组大小，并通过交互式可视化和基于分类的摘要呈现结果，从而能够快速洞察。该管道针对工作站和计算集群的所有步骤都实现了自动化。EzMap 自动化了原本繁琐且耗时的协议，旨在促进从 cfDNA 中快速获得可重复的见解。
EzMap 可在 https://github.com/dekoning-lab/ezmap 上免费获得。
补充数据可在“Bioinformatics”在线获取。
