BacterialTyper
BacterialTyper: a bioinformatics pipeline for the integrative analysis of bacterial WGS
Table of Contents
Introduction
We present BacterialTyper, a pipeline for the analysis of bacterial WGS data that integrates and facilitates the interpretation of results generated from multiple software analysis. It is capable of processing and identifying bacterial strains, identifying resistance and virulence genes, and generating data for outbreak analysis using WGS data from isolated microbial cultured colonies. The design of this bioinformatic tool allows comparing samples with an internal database (previously identified samples) and external databases.
The pipeline is written in Python with a modular architecture and based on open-source software and databases engines. Multiple tasks are performed by each of several modules including: preparation of raw data; assembly and annotation; bacterial strain identification; mobile genetic elements identification (plasmids, putative pathogenicity islands or phage insertions regions); generation of a virulence and resistance profile; clustering based on sequence similarity; phylogenetic analysis; integration of metadata, etc. The tool allows to compare samples with previously identified samples (collected and internal database) but it also uses, and updates periodically, external databases from different sources.
Installation
To install BacterialTyper you need to create a conda environment with all dependendies requiere. In following weeks/months a stable conda recipe will be available.
We recommend using mamba to solve all dependencies and conflicts. To install mamba simply type in the base environemt:
## create environment and activate it
conda create -y -n BacterialTyper
conda activate BacterialTyper
## install mamba
conda install -c conda-forge mamba
Then, use mamba instead of conda to install further packages.
So far, you can either install BacterialTyper using:
- a configuration file within this git repository (BacterialTyper/devel/conda/bacterialtyper-list.txt). See file here
- or typing the following conda/mamba command:
mamba install -c r -c bioconda -c conda-forge \
perl-bio-searchio-hmmer perl-bioperl \
trimmomatic fastqc spades snippy prokka kma \
agrvate staphopia-sccmec kraken2 bowtie2 \
ncbi-amrfinderplus bracken krakentools mlst
Finally, you will need to install BacterialTyper which is host in pypi here. Use pip and type:
pip install BacterialTyper
This will create a working installation of BacterialTyper and all dependencies.
Verify the configuration using
BacterialTyper config check
Documentation
For a full documentation and details visit Read the Docs site here.
License
MIT License
Copyright (c) 2020-2022 HCGB-IGTP
See additional details here
Citation
BacterialTyper was initially described in the ECCMID 2020 Poster [1]. See and example of usage in the characterization of some clinical samples [2].
[1] Sanchez-Herrero, J.; Lacoma, A.; Molina-Moya, B.; Giménez, M.; Molinos, S.; Prat, C.; Sumoy, L. BacterialTyper: A Bioinformatics Pipeline for the Integrative Analysis of Bacterial Whole Genome Sequencing. Abstract 1981. In Proceedings of the 30th European Congress of Clinical Microbiology and Infectious Diseases, Paris, France, 18–21 April 2020
[2] A. Lacoma et al., “Genotypic and Phenotypic Characterization of Staphylococcus aureus Isolates from the Respiratory Tract in Mechanically-Ventilated Patients,” Toxins (Basel)., vol. 13, no. 2, p. 122, Feb. 2021.