sciReptor: analysis of single-cell level immunoglobulin repertoires.
sciReptor: analysis of single-cell level immunoglobulin repertoires.
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DOI：
10.1186/s12859-016-0920-1
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发表时间：
2016-02-04
影响因子：
3
通讯作者：
Busse CE
中科院分区：
文献类型：
--
作者：
Imkeller K;Arndt PF;Wardemann H;Busse CE
来自单个B细胞的免疫球蛋白（IG）转录物的测序产生关于IG重链：轻链配对的基本信息，这在常规批量测序实验中丢失。单细胞方法先前有限的通量最近已经通过引入多个基于下一代测序（NGS）的平台而被克服。此外，单细胞技术允许分配额外的数据类型（例如细胞表面标志物表达），这对于生物学解释至关重要。然而，目前可用的计算工具不是设计来处理单细胞数据，并且不提供用于将序列数据与其他生物数据相关联的整体解决方案。在这里，我们介绍sciReptor，一个灵活的工具包，用于在单细胞水平上处理和分析抗原受体库测序数据。该软件将免疫球蛋白序列注释的生物信息学工具与关系数据库相结合，在关系数据库中存储和链接原始数据和分析结果。sciReptor支持附加数据类别的属性，例如细胞表面标记表达或免疫学元数据。此外，它还包括一个质量控制模块以及基本的剧目可视化工具。sciReptor是一个灵活的框架，用于在单细胞水平上对抗原受体库进行标准化序列分析。关系数据库允许轻松的数据共享和下游分析，以及不同数据集之间的即时比较。本文的在线版本（doi：10.1186/s12859-016-0920-1）包含补充材料，可供授权用户使用。
The sequencing of immunoglobulin (Ig) transcripts from single B cells yields essential information about Ig heavy:light chain pairing, which is lost in conventional bulk sequencing experiments. The previously limited throughput of single-cell approaches has recently been overcome by the introduction of multiple next-generation sequencing (NGS)-based platforms. Furthermore, single-cell techniques allow the assignment of additional data types (e.g. cell surface marker expression), which are crucial for biological interpretation. However, the currently available computational tools are not designed to handle single-cell data and do not provide integral solutions for linking of sequence data to other biological data. Here we introduce sciReptor, a flexible toolkit for the processing and analysis of antigen receptor repertoire sequencing data at single-cell level. The software combines bioinformatics tools for immunoglobulin sequence annotation with a relational database, where raw data and analysis results are stored and linked. sciReptor supports attribution of additional data categories such as cell surface marker expression or immunological metadata. Furthermore, it comprises a quality control module as well as basic repertoire visualization tools. sciReptor is a flexible framework for standardized sequence analysis of antigen receptor repertoires on single-cell level. The relational database allows easy data sharing and downstream analyses as well as immediate comparisons between different data sets. The online version of this article (doi:10.1186/s12859-016-0920-1) contains supplementary material, which is available to authorized users.