STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication.

Bioinformatics (Oxford, England) Pub Date : 2024-11-26 DOI:10.1093/bioinformatics/btae713

Jared M Andrews, Michael W Lloyd, Steven B Neuhauser, Margaret Bundy, Emily L Jocoy, Susan D Airhart, Carol J Bult, Yvonne A Evrard, Jeffrey H Chuang, Suzanne Baker

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Abstract

Summary: Short tandem repeat (STR) profiling is commonly performed for authentication of biomedical models of human origin, yet no tools exist to easily compare sets of STR profiles to each other or an existing database in a high-throughput manner. Here, we present STRprofiler, a Python package, command line tool, and Shiny application providing methods for STR profile comparison and cross-contamination detection. STRprofiler can be run with custom databases or used to query against the Cellosaurus cell line database.

Availability and implementation: STRprofiler is freely available as a Python package with a rich CLI from PyPI https://pypi.org/project/strprofiler/ with source code available under the MIT license on GitHub https://github.com/j-andrews7/strprofiler and at https://zenodo.org/records/10989034. A web server hosting an example STRprofiler Shiny application backed by a database with data from the National Cancer Institute-funded PDXNet consortium and The Jackson Laboratory PDX program is available at https://sj-bakerlab.shinyapps.io/strprofiler/. Full documentation is available at https://strprofiler.readthedocs.io/en/latest/.

Supplementary information: Supplementary data are available at Bioinformatics online.

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STRprofiler：用于生物医学模型认证的短串联重复谱的高效比较。

摘要：短串联重复（STR）图谱分析通常用于验证人类来源的生物医学模型，但目前还没有工具能以高通量的方式轻松地将各组 STR 图谱相互比较或与现有数据库进行比较。在这里，我们介绍 STRprofiler，它是一个 Python 软件包、命令行工具和 Shiny 应用程序，提供了 STR 图谱比较和交叉污染检测的方法。STRprofiler 可与自定义数据库一起运行，也可用于查询 Cellosaurus 细胞系数据库：STRprofiler 是一个 Python 软件包，带有丰富的 CLI，可从 PyPI https://pypi.org/project/strprofiler/ 免费获取，源代码在 MIT 许可下可从 GitHub https://github.com/j-andrews7/strprofiler 和 https://zenodo.org/records/10989034 获取。STRprofiler Shiny 应用程序示例的网络服务器托管于一个数据库，该数据库的数据来自美国国立癌症研究所资助的 PDXNet 联盟和杰克逊实验室的 PDX 项目，可在 https://sj-bakerlab.shinyapps.io/strprofiler/ 上获取。完整的文档可在 https://strprofiler.readthedocs.io/en/latest/.Supplementary 信息中获取：补充数据可在 Bioinformatics online 上获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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