ECTyper
What does it do?
Use ECTyper to predict the O-antigen and H-antigen serotype of Escherichia coli draft genome assemblies.
ECTyper reports predicted O-type, H-type, and supporting allele evidence. It is specific to E. coli serotyping and does not replace MLST sequence typing or broad organism identification.
The source code is available in the PHAC-NML ECTyper repository.
How do I use it?
Subject
In the Subject field, enter:
ec_typer
Spelling matters, but matching is not case-sensitive.
Description
Enter one E. coli assembly SEQID per line:
2026-SEQ-0001
2026-SEQ-0002
Attachments
No attachment is required. ECTyper retrieves the draft assembly associated with each requested SEQID.
Optional parameters
The supplied documentation does not identify optional parameters for the Redmine ECTyper automator.
Example
See issue 15946 for an example ECTyper request.
Interpreting results
ECTyper uploads:
ec_typer_report.tsv
The report includes the sample name, predicted O-type, predicted H-type, and supporting allele results. Example:
| Name | O-type | H-type | O-antigen allele evidence | Additional O-antigen evidence | H-antigen allele evidence |
|---|---|---|---|---|---|
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 |
A dash (-) means that ECTyper did not assign that serotype component. In the example above, 2019-SEQ-0145 has an H-type prediction but no O-type prediction.
The allele values provide supporting match evidence for loci such as wzx, wzy, and fliC. Interpret partial or discordant support cautiously and review assembly quality when an expected O-type or H-type is missing.
How long does it take?
ECTyper generally takes approximately one minute per genome. Total runtime depends on the number of requested assemblies and service workload.
What can go wrong?
A requested SEQID is unavailable
Symptom: The Redmine issue receives a warning identifying unavailable assemblies.
Likely cause: ECTyper cannot locate the draft assembly associated with the requested SEQID.
What to do: Verify each SEQID, confirm that its assembly is available, and submit a corrected request.
The requested assembly is not E. coli
Symptom: The report is missing, uninformative, or does not provide meaningful O- and H-type predictions.
Likely cause: ECTyper is designed for Escherichia coli assemblies.
What to do: Confirm the organism before interpreting the result. Use an identification workflow such as Unknown Isolate when species identity is uncertain.
An O-type or H-type is not assigned
Symptom: The report shows - for one serotype component.
Likely cause: The required allele was not detected with sufficient support, the assembly is incomplete, or the serotype is not represented adequately by the method.
What to do: Review the supporting allele fields and assembly quality before drawing conclusions.
Related automators
- MLST — determines an E. coli sequence type using a selected Achtman or Pasteur scheme.
- Unknown Isolate — investigates uncertain genus or species identity using rMLST, MASH, and ANI.
- IntiminTyper — performs intimin typing for supported E. coli analyses.