XspecT 0.5.2

Tool to monitor and characterize pathogens using Bloom filters.

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 the lastest 64 bit Python version 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