kbessonov/ectyper repository overview

This is repository of the ECTyper tool⁠ designed to serotype E.coli. To execute this image and perform analysis in a container, mount the directory containing inputs (assembled or raw genomes) and execute typing commands as shown below. The results should be written to the mounted directory, otherwise they will disappear upon container closure.

docker run -it --rm -v <directory with genomes>:/ectyper kbessonov/ectyper:1.0.0  bash -c "cd /ectyper && ectyper -i input.fasta --verify -o ectyper-report"

where <directory with genomes> is an absolute path to the folder containing your input (e.g. genomes in a FASTA format) and input.fasta is an input genome (ECTyper also supports multiple file inputs by specifying a directory name of a current location such as . or directory name. All valid input files will be typed by the tool and invalid ones skipped). The output will be written to that directory in theectyper-report folder.

Results are found in the tab-delimited output.tsv file

The tool is also available online at https://usegalaxy.eu/root?tool_id=ectyper⁠