VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
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DOI：
10.1371/journal.pcbi.1004503
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发表时间：
2015-11
影响因子：
4.3
通讯作者：
Chudakov DM
中科院分区：
文献类型：
--
作者：
Shugay M;Bagaev DV;Turchaninova MA;Bolotin DA;Britanova OV;Putintseva EV;Pogorelyy MV;Nazarov VI;Zvyagin IV;Kirgizova VI;Kirgizov KI;Skorobogatova EV;Chudakov DM
尽管越来越多的免疫库测序研究，该领域仍然缺乏分析和理解这种高维数据的软件。在这里，我们报告VDJtools，一个互补的软件套件，解决了广泛的T细胞受体（TCR）剧目后分析任务，提供了详细的表格输出和出版准备图形，并建立在一个灵活的API。使用TCR数据集的一个大的队列无关的健康供体，双胞胎和多发性硬化症患者，我们证明了VDJtools极大地促进了分析，并导致健全的生物学结论。VDJtools软件和文档可从https://github.com/mikessh/vdjtools获得。T细胞和B细胞抗原受体库的高通量分析有望在我们理解适应性免疫系统功能的机制、自身免疫和感染性疾病的治疗以及癌症免疫治疗新方法的开发方面取得巨大进展。许多最近开发的软件工具旨在通过将可变（V）、多样性（D）和连接（J）抗原受体区段映射到测序读段并组装T细胞和B细胞克隆型来处理免疫库数据。然而，在外地数据后分析的通用方法方面仍然存在重大差距：迄今为止没有标准化的数据格式，大多数数据比较分析是使用各种内部脚本进行的。在这里，我们介绍了VDJtools，这是一个软件框架，可以分析最常用的TCR库处理工具的输出，并允许应用一组不同的后分析策略。我们的框架的主要目标是：为了确保后分析方法的一致性和获得的结果的可重复性;通过提供全面的表格输出和开源API来节省生物信息学家分析TCR库数据的时间;并提供一个足够简单的命令行工具，以便几乎没有计算背景的免疫学家和生物学家可以使用它来生成可发表的结果。
Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools. High-throughput profiling of T- and B-cell antigen receptor repertoires promises great advances in our understanding of the mechanisms underlying adaptive immune system function, treatment of autoimmune and infectious diseases, and development of novel approaches in cancer immunotherapy. A number of recently developed software tools aim at processing immune repertoire data by mapping Variable (V), Diversity (D) and Joining (J) antigen receptor segments to sequencing reads and assembling T- and B-cell clonotypes. Nevertheless, there still exists a major gap in common methods of data post-analysis in the field: there is no standardized data format so far, and most of data comparative analysis is carried out using a variety of in-house scripts. Here we present VDJtools, a software framework that can analyze output of most commonly used TCR repertoire processing tools and allows applying a diverse set of post-analysis strategies. The main aims of our framework are: To ensure consistency of post-analysis methods and reproducibility of obtained results; to save the time of bioinformaticians analyzing TCR repertoire data by providing comprehensive tabular output and open-source API; and to provide a simple enough command line tool so that immunologists and biologists with little computational background could use it to generate publication-ready results.