ECTyper

What does it do?

The ECTyper automator performs serotyping on FASTA files.

Check out the source code: github

How do I use it?

Subject

In the Subject field, put ec_typer. Spelling counts, but case sensitivity does not.

Description

All you need to put in the description is a list of SEQIDs you want to process, one per line.

Example

For an example ECTyper analysis, see issue 15946.

Interpreting Results

ECTyper will output a summary report, ec_typer_report.tsv ,that should look something like the following:

Name	O-type	H-type	Alleles
2014-SEQ-0276	O157	H7	wzx: 1.00	wzy: 0.58	fliC: 1.00
2019-SEQ-0137	O146	H8	wzx: 1.00	wzy: 0.56	fliC: 1.00
2019-SEQ-0145	-	H2	fliC: 1.00

How long does it take?

ECTyper is pretty fast - expect it to take a minute per genome you give it.

What can go wrong?

1. Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.