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:

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:

Additional species models can be trained using:

How to run the web app

To run the web app, simply execute:

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:

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: