pybamview
Browser based application for viewing bam alignments
The website is here and contains full usage instructions, an faq, and a served example.
Copyright (c) 2014 Melissa Gymrek mgymrek@mit.edu
LICENSE: MIT (see LICENSE.txt)
Requirements
PyBamView requires Python2.7 or greater. The following python packages are required:
Flaskpysampyfastapandas
These can all be installed using pip or easy_install. Additionally, the package rsvg-convert is required for exporting alignment snapshots to PDF.
Installation
PyBamView can be easily installed using pip: easy_install pybamview
To install from source, download or clone the package from github, ensure the required packages are installed, and run python setup.py install from the root directory of the pybamview package.
Usage
To use PyBamView, you will need a directory containing indexed BAM files, and optionally a reference genome. All reads in the BAM files must be annotated with a read group. To run, type the command:
pybamview --bamdir $BAMDIR --ref $REF.FA
This will serve pybamview at http://127.0.0.1:5000. Navigate to this URL at your web browser, where you can select samples and start visualizing alignments. Use the --ip and --port to change the host URL and port if desired.