JBrowse Jupyter: a Python interface to JBrowse 2

Motivation: JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization.Results: We have developed a package that provides a Python interface to JBrowse 2's suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google's Colab notebooks, providing reproducible interactive views.

Automated summary

JBrowse Jupyter is a package that aims to bridge the gap between Python programming and genomic visualization. It provides a Python interface to quickly set up, launch and customize JBrowse views in Jupyter notebooks. Users can also share their data through Google's Colab notebooks, ensuring reproducible interactive views.