An app written in Python3 using Bokeh to visualise raw squiggle data from Oxford Nanopore Technologies (ONT) bulkfiles. See the documentation at https://bulkvis.readthedocs.io
# Make a python3 virtual environment
$ mkdir ~/envs
$ cd ~/envs
$ python3 -m venv ~/envs/bulkvis
# Activate virtual environment
$ source ~/envs/bulkvis/bin/activate
# Clone the repo to your installation/projects directory
$ git clone https://github.com/LooseLab/bulkvis.git
# Enter the bulkvis folder
$ cd bulkvis
# Install dependencies via pip
$ pip install -r requirements.txt
# Set config with set_config.py
$ python utils/set_config.py -b <<bulkfile>> -i /path/to/bulkfile/directory -e /path/to/readfile/directory -m /path/to/mapfile/directory -c config.ini
# Move to bulkvis' parent folder
$ cd ..
# Start bokeh server
$ bokeh serve --show bulkvis
bulkvis uses some user defined parameter to set default plot options. These can change depending on your preferences. For a comprehensive overview of the config file see config.md