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.
STRprofiler is freely available as a Python package with a rich CLI from PyPI with source code available under the MIT license on GitHub. 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 here. Full documentation is available on ReadTheDocs.
Read more the methodology in our paper.
