ECTyper is a standalone versatile serotyping module for Escherichia coli. It supports both fasta (assembled) and fastq (raw reads) file formats. The tool provides convenient species identification coupled to quality control module giving a complete, transparent and reference laboratories suitable report on E.coli serotyping, Shiga toxin typing and pathotyping.

• Version: 2.0.0
• Added: August, 2025
• Link: https://github.com/phac-nml/ecoli_serotyping

See which versions are available:

$ module avail ectyper

Load one version into your environment and run it:

$ module load ectyper/2.0.0
$ ectyper -h

Notes from the sysadmin during installation:

$ cd /var/scratch
$ git clone https://github.com/phac-nml/ecoli_serotyping.git -b v2.0.0
$ module load python/3.10
$ sudo mkdir -p /export/apps/ectyper/2.0.0
$ sudo chown aorth /export/apps/ectyper/2.0.0
$ python -m venv /export/apps/ectyper/2.0.0
$ source /export/apps/ectyper/2.0.0/bin/activate
$ python -m pip install -U pip setuptools wheel
$ python -m pip install .
$ sudo chown -R root:root /export/apps/ectyper

Note: the dependencies are not specified well on the GitHub README.md so I used the Conda environment as a reference: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/ectyper/meta.yaml