IntiminTyper

What does it do?

IntiminTyper uses phylotyper developed at the Public Health Agency of Canada to assign subtypes to intimin (eae) genes in Escherichia coli.

How do I use it?

Subject

In the Subject field, put intimin_typer. Spelling counts, but case sensitivity doesn't.

Description

All you need to put in the description is a list of SEQIDs you want to subtype intimin genes in, one per line. Nothing bad will happen if you put in SEQIDs that aren't from E. coli, but you won't get any results for those SeqIDs.

Example

For an example IntiminTyper, see issue 16512.

Interpreting Results

IntiminTyper will upload a file called intimin_predictions.tsv - this file will tell what subtype the intimin gene in each of your samples is, noting if it's an exact match to a known allele or a guess based on what the allele is similar to. When IntiminTyper guesses you'll also receive a probability showing how certain it is with its guess.

How long does it take?

IntiminTyper should take about 30 seconds for analysis of each sample.

What can go wrong?

1) Requested SEQIDs are not available: If we can't find some of the SEQIDs that you request, they won't show up in your final report.