XspecT - Acinetobacter Species Assignment Tool

XspecT is a Python-based tool to taxonomically classify Acinetobacter 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.

Table of Content

• Installation and Usage
  • Python Modules - Install Requirements
  • List of used Modules for Python (3.10):
  • How to run the web-app: Local Deployment
• Input Data
• Walkthrough
• Contributors
• About this project

Installation and Usage

Python Modules - Install Requirements

On Linux you need the python-dev package:

sudo apt install python3.10-dev

XspecT requires the latest 64 bit Python version and a list of Python Modules (see below).

pip install -r requirements.txt

List of used Modules for Python (3.10):

• Flask
• Flask-Bcrypt
• Flask-Login
• Flask-WTF
• WTForms
• Werkzeug
• Bcrypt
• Biopython
• bitarray
• mmh3
• numpy
• pandas
• requests
• scikit-learn
• Psutil
• Matplotlib
• Pympler
• H5py

Get the Bloomfilters

Copy the folder that is located in the following directory into your XspecT installation:

/share/project/dominik_s/XspecT/

How to run the web-app: Local Deployment

Run the following command lines in a console, a browser window will open automatically after the application is fully loaded.

MAC/Linux:

$ export FLASK_APP=flaskr
$ export FLASK_ENV=development
$ python app.py

Windows cmd:

set FLASK_APP=flaskr
set FLASK_ENV=development
python app.py

How to use the XspecT command line interface:

Open the file XspecT_mini.py with the configuration you want to run it with as arguments.

python3 XspecT_mini.py XspecT ClAssT Oxa Fastq 100000 Metagenome "path/to/your/input-set"

Important:

• If you use reads the number of reads needs to specified directly after the file-type
• the path to your data-set is the last argument
• all commands are explained in XspecT_mini Commands/.md

Input Data

XspecT is able to use either raw sequence-reads (FASTQ-format .fq/.fastq) or already assembled genomes (FASTA-format .fasta/.fna). Using sequence-reads saves up the assembly process but high-quality reads with a low error-rate are needed (e.g. Illumina-reads).

The amount of reads that will be used has to be set by the user when using sequence-reads. The minimum amount is 5000 reads for species classification and 500 reads for sub-type classification. The maximum number of reads is limited by the browser and is usually around ~8 million reads. Using more reads will lead to a increased runtime (xsec./1mio reads).

Walkthrough

A detailed walkthrough with examples is provided in Xspect’s wiki.

Contributors

• Sam Gimbel
• Bardja Djahanschiri
• Vinh Tran
• Ingo Ebersberger

About this project

This project is an attempt to support hospital staff in a possible A. baumannii outbreak. A. baumannii can build up antibiotic resistance and can cause deadly nosocomial infections. This is a bachelor thesis project; no warranty is given. Check the license for more information. constructive criticism/feedback always welcomed!