LooseLab / bulkvis

⇜ bulkvis ⇝

An app written in Python3 using Bokeh to visualise raw squiggle data from Oxford Nanopore Technologies (ONT) bulkfiles.

Quickstart

Our preferred installation method uses conda with this environment setup:

name: bulkvis
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - python=3.11
  - pip
  - pip:
    - git+https://github.com/LooseLab/bulkvis.git@2.0

Either copy the YAML above into a file or:

curl -O https://raw.githubusercontent.com/LooseLab/bulkvis/2.0/env.yml
conda env create -f env.yml

Then bulkvis can be started using:

conda activate bulkvis
bulkvis serve <BULK_FILE_DIRECTORY> --show

or with another python source

# Make a python3 virtual environment
python3 -m venv bulkvis

# Activate virtual environment
source bulkvis/bin/activate

# Clone the repo to your installation/projects directory
pip install git+https://github.com/LooseLab/bulkvis.git@2.0

# Start bokeh server
bulkvis serve <BULK_FILE_DIRECTORY> --show

Other install requires:

To open some bulk FAST5 files vbz compression plugins are required. These are written and maintained by Oxford Nanopore Technologies.