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.
From a Python environment that has Python 3.6 or later installed you can easily
$ pip install sanger-sequencing
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 (
You can find the complete documentation at: https://sanger-sequencing.readthedocs.io.
- Copyright (c) 2018 Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark licensed under the Apache License, Version 2.0