a-slide / Fast5Tools

Tools to manipulate Fast5 files

Fast5Tools 0.3.1 package documentation

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Fast5 tools is a collection of tools to manipulate Fast5 files

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• Author: Adrien Leger - aleg {at} ebi.ac.uk

• URL: https://github.com/a-slide/Fast5Tools

• Licence: GPLv3

• Python version: >=3.3

Installation

Ideally, before installation, create a clean python3 virtual environment to deploy the package, using virtualenvwrapper for example (see http://www.simononsoftware.com/virtualenv-tutorial-part-2/).

Required python packages:

All dependencies are automatically installed if using pip

• h5py>=2.7.0
• numpy==1.14.0
• matplotlib>=2.0.0
• pysam>=0.12.0
• pandas>=0.23.0

Installation with pip

Ideally, before installation, create a clean python3 virtual environment to deploy the package, using virtualenvwrapper for example (see http://www.simononsoftware.com/virtualenv-tutorial-part-2/).

• To install the package

  pip3 install git+https://github.com/a-slide/Fast5Tools.git

• To update the package:

  pip3 install git+https://github.com/a-slide/Fast5Tools.git --upgrade

Usage and tests

TO DO

Fast5Tools --help