XspecT 0.2.4

Tool to monitor and characterize pathogens using Bloom filters.

XspecT - Acinetobacter Species Assignment Tool

XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or sub-type level using Bloom Filters and a Support Vector Machine. It also identifies existing blaOxa-genes and provides a list of relevant research papers for further information.

XspecT utilizes the uniqueness of kmers and compares extracted kmers from the input-data to a reference database. Bloom Filter ensure a fast lookup in this process. For a final prediction the results are classified using a Support Vector Machine.

Local extensions of the reference database are supported.

The tool is available as a web-based application and a smaller 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 is currently not supported.

Usage

Get the Bloomfilters

To download basic pre-trained filters, you can use the built-in command:

xspect download-filters

Additional species filters can be trained using:

xspect train you-ncbi-genus-name

How to run the web app

To run the web app, install and run XspecT Web. Additionally, run XspecT in API mode:

xspect api

How to use the XspecT command line interface

Run xspect with the configuration you want to run it with as arguments.

xspect classify your-genus path/to/your/input-set

For further instructions on how to use the command line interface, please refer to the documentation or execute:

xspect --help