ngsderive
Forensic analysis tool useful in backwards computing information from next-generation sequencing data and annotating splice junctions.
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Notice:
ngsderiveis largely a forensic analysis tool useful in backwards computing information from next-generation sequencing data. Notably, most results are provided as a 'best guess' — the tool does not claim 100% accuracy and results should be considered with that understanding. An exception would be thejunction-annotationtool which analyzes more concrete evidence than the other tools.
🎨 Features
The following attributes can be guessed using ngsderive:
- Illumina Instrument. Infer which Illumina instrument was used to generate the data by matching against known instrument and flowcell naming patterns. Each guess comes with a confidence score.
- RNA-Seq Strandedness. Infer from the data whether RNA-Seq data was generated using a Stranded-Forward, Stranded-Reverse, or Unstranded protocol.
- Pre-trimmed Read Length. Compute the distribution of read lengths in the file and attempt to guess what the original read length of the experiment was.
- PHRED Score Encoding. Infers which encoding scheme was used to store PHRED scores as ASCII characters.
- Junction Annotation. Annotates splice junctions as novel, partial novel, or known in comparison to a reference gene model.
📚 Getting Started
Installation
You can install ngsderive using the Python Package Index (PyPI).
pip install ngsderive🖥️ Development
If you are interested in contributing to the code, please first review our CONTRIBUTING.md document.
To bootstrap a development environment, please use the following commands.
# Clone the repository
git clone git@github.com:stjudecloud/ngsderive.git
cd ngsderive
# Install the project using poetry
poetry install🚧️ Tests
ngsderive provides a (currently patchy) set of tests — both unit and end-to-end.
py.test🤝 Contributing
Contributions, issues and feature requests are welcome!
Feel free to check issues page. You can also take a look at the contributing guide.
📝 License
This project is licensed as follows:
- All code related to the
instrumentsubcommand is licensed under the AGPL v2.0. This is not due to any strict requirement, but out of deference to some code I drew inspiration from (and copied patterns from), the decision was made to license this code consistently. - The rest of the project is licensed under the MIT License - see the LICENSE.md file for details.
Copyright © 2020 St. Jude Cloud Team.