# *Escherichia coli*

## Usage
 
The workflow is designed for analysis of *Escherichia coli* (including ETEC, EIEC, and EPEC) and *Shigella* spp.

## Supported analysis

The workflow includes the following analysis in addition to species prediction and various methods for assessing the sequencing quality,

- Antibiotic resistance prediction
- Disinfectant resistance
- Prediction of virulence factors
- Plasmid detection
- STX typing
- Serotyping
- Discrimination between ETEC, EIEC, EPEC, and *Shigella*
- MLST
- cgMLST

## Software & database versions

```{csv-table} Versions of softwares and containers used by the *Escherichia coli* workflow.
:file: escherichia_coli_sw.csv

```