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免疫数据库（ImmuneDB）：一种用于免疫受体测序数据分析、存储和传播的新型工具。

ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data.

机构信息

School of Biomedical Engineering Science and Health Systems, Drexel University, Philadelphia, PA, United States.

Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.

出版信息

Front Immunol. 2018 Sep 21;9:2107. doi: 10.3389/fimmu.2018.02107. eCollection 2018.

DOI:10.3389/fimmu.2018.02107
PMID:30298069
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6161679/
Abstract

ImmuneDB is a system for storing and analyzing high-throughput immune receptor sequencing data. Unlike most existing tools, which utilize flat-files, ImmuneDB stores data in a well-structured MySQL database, enabling efficient data queries. It can take raw sequencing data as input and annotate receptor gene usage, infer clonotypes, aggregate results, and run common downstream analyses such as calculating selection pressure and constructing clonal lineages. Alternatively, pre-annotated data can be imported and analyzed data can be exported in a variety of common Adaptive Immune Receptor Repertoire (AIRR) file formats. To validate ImmuneDB, we compare its results to those of another pipeline, MiXCR. We show that the biological conclusions drawn would be similar with either tool, while ImmuneDB provides the additional benefits of integrating other common tools and storing data in a database. ImmuneDB is freely available on GitHub at https://github.com/arosenfeld/immunedb, on PyPi at https://pypi.org/project/ImmuneDB, and a Docker container is provided at https://hub.docker.com/r/arosenfeld/immunedb. Full documentation is available at http://immunedb.com.

摘要

ImmuneDB 是一个用于存储和分析高通量免疫受体测序数据的系统。与大多数使用平面文件的现有工具不同，ImmuneDB 将数据存储在结构良好的 MySQL 数据库中，从而能够实现高效的数据查询。它可以接受原始测序数据作为输入，并注释受体基因的使用情况，推断克隆型，聚合结果，并运行常见的下游分析，如计算选择压力和构建克隆谱系。或者，可以导入预先注释的数据，并以多种常见的适应性免疫受体库 (AIRR) 文件格式导出分析数据。为了验证 ImmuneDB，我们将其结果与另一个管道 MiXCR 进行了比较。我们表明，使用这两种工具得出的生物学结论是相似的，而 ImmuneDB 提供了集成其他常见工具和将数据存储在数据库中的额外优势。ImmuneDB 可在 GitHub 上的 https://github.com/arosenfeld/immunedb、PyPi 上的 https://pypi.org/project/ImmuneDB 以及 https://hub.docker.com/r/arosenfeld/immunedb 上的 Docker 容器中免费获得。完整的文档可在 http://immunedb.com 上获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/672b/6161679/935ac7431565/fimmu-09-02107-g0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/672b/6161679/354e585bbf4c/fimmu-09-02107-g0001.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/672b/6161679/9c7381b625f8/fimmu-09-02107-g0005.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/672b/6161679/935ac7431565/fimmu-09-02107-g0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/672b/6161679/354e585bbf4c/fimmu-09-02107-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/672b/6161679/8770ed0096d4/fimmu-09-02107-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/672b/6161679/53a356edc8a4/fimmu-09-02107-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/672b/6161679/75cc0e5d2018/fimmu-09-02107-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/672b/6161679/9c7381b625f8/fimmu-09-02107-g0005.jpg
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