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Jupyter Notebooks extension for showing JBrowse views

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JBrowse Jupyter

JBrowse Jupyter is a python package that let's you create JBrowse 2 views in Jupyter notebooks


  • Basic usage - Open In Colab
  • SKBR3 cancer cell line demo - Open In Colab



More documentation here


$ pip install jbrowse-jupyter



See our contributing guide.


JBrowse Jupyter: a Python interface to JBrowse 2, Bioinformatics (2023)

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What file types are supported?

We currently support:

  • bam/cram
  • bigwig
  • bigbed
  • indexed fasta/bgzip indexed fasta
  • twobit
  • gff3 tabix
  • vcf/vcf tabix

How do I configure text searching?

In order to configure text searching in your Linear Genome View, you must first create a text index. Follow the steps found here. Then you must create and add a text search adapter to your config.

Can I use local files/my own data?

Yes, there are a couple of ways in which you can configure and use your own data from your local environment in jbrowse views. 1. Make use of the jupyter notebook/lab server. Intended for those running their notebooks with jupyter lab or jupyter notebook. 2. Launch your own http server with CORS which will enable you to use local files. You can run our to launch our dev server. (Checkout our local_support.ipynb for tutorials on how to use your own data)

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