This project has been archived by its maintainers, and is no longer receiving any updates.
ngsderive
Forensic analysis tool useful in backwards computing information from next-generation sequencing data and annotating splice junctions.
Explore the docs »
Request Feature
·
Report Bug
·
⭐ Consider starring the repo! ⭐
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.
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file ngsderive-4.0.0.tar.gz.
File metadata
- Download URL: ngsderive-4.0.0.tar.gz
- Upload date:
- Size: 20.8 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/3.8.0 pkginfo/1.9.6 readme-renderer/40.0 requests/2.31.0 requests-toolbelt/1.0.0 urllib3/2.0.4 tqdm/4.66.1 importlib-metadata/6.8.0 keyring/24.2.0 rfc3986/2.0.0 colorama/0.4.6 CPython/3.8.18
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
1e55f7bed3dfe1ecf4b3955636bd6fc7b1c1bd7c5685c539c0e248abfc47bf97
|
|
| MD5 |
a9634e41f0f660eb86b0aeb88df487dd
|
|
| BLAKE2b-256 |
a82d5cd92e2f05188a46b270ee5227cc391ce86f783459d1d25582b96e810530
|
File details
Details for the file ngsderive-4.0.0-py3-none-any.whl.
File metadata
- Download URL: ngsderive-4.0.0-py3-none-any.whl
- Upload date:
- Size: 23.4 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/3.8.0 pkginfo/1.9.6 readme-renderer/40.0 requests/2.31.0 requests-toolbelt/1.0.0 urllib3/2.0.4 tqdm/4.66.1 importlib-metadata/6.8.0 keyring/24.2.0 rfc3986/2.0.0 colorama/0.4.6 CPython/3.8.18
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
afef89cde8fd7d61c432b5b1911365afdc10a735541a71b563686f7db6eae714
|
|
| MD5 |
408b0f603a7532817f19c748f16af124
|
|
| BLAKE2b-256 |
2f8e13e17561491a7ff810f6d51f6e4253a7cc4e025dad361cb392d037ee7aa6
|
