XspecT
XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or MLST level using kmer indices and a support vector machine.
XspecT utilizes the uniqueness of kmers and compares extracted kmers from the input-data to a kmer index. Probablistic data structures ensure a fast lookup in this process. For a final prediction, the results are classified using a support vector machine.
The tool is available as a web-based application and as a command line interface.
Installation
To install XspecT, please download Python 3.10 - 3.13 and install the package using pip:
pip install xspect
Please note that Windows and Alpine Linux are currently not supported.
Usage
Get the models
To download basic pre-trained models, you can use the built-in command:
xspect models download
Additional species models can be trained using:
xspect models train ncbi
How to run the web app
To run the web app, simply execute:
xspect web
This will start a local web server. You can access the web app by navigating to http://localhost:8000 in your web browser.
How to use the XspecT command line interface
To use the XspecT command line interface, execute xspect with the desired subcommand and parameters.
Example:
xspect classify species
If you do not provide the required parameters, the command line interface will prompt you for them. For further instructions on how to use the command line interface, please refer to the documentation or execute:
xspect --help
1 maintainer
Release files for XspecT 0.7.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| xspect-0.7.6.tar.gz | 527.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| xspect-0.7.6-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.1 MB
Release files / xspect-0.7.6.tar.gz
| Download URL | xspect-0.7.6.tar.gz |
|---|---|
| Size | 527.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Transparency logRelease files / xspect-0.7.6-py3-none-any.whl
| Download URL | xspect-0.7.6-py3-none-any.whl |
|---|---|
| Size | 523.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
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