Sanger Sequence Analysis

Semi-automated Sanger sequence analysis for plasmid verification.

This package is the result of an internal hackathon at the Novo Nordisk Foundation Center for Biosustainability and represents our approach to improving the workflow of geneticists who need to verify plasmid constructs by Sanger sequencing.

Getting Started

From a Python environment that has Python 3.6 or later installed you can easily

$ pip install sanger-sequencing

or use pip3 depending on your environment.

When you import the package, two main components are made available to you: a configuration class that you can instantiate to set some global configuration values and a high level analysis interface.

import sanger_sequencing

config = sanger_sequencing.Configuration()
print(config.threshold)
print(config.output)

You can read more about the meaning of those attributes in the configuration documentation. The main entry point for doing any kind of analysis is the sanger_verification function. This function requires three arguments: a template table of what to analyze, a mapping from plasmid identifiers to their sequence records (typically coming from Genbank files), and a mapping from sample identifiers to sequence records (.ab1 files).

You can find the complete documentation at: https://sanger-sequencing.readthedocs.io.

Copyright

• Copyright (c) 2018 Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark licensed under the Apache License, Version 2.0

Credits

This package was created using cookiecutter and the DD-DeCaF/cookiecutter-decaf-python project template.