LpST_ONTmompS.tsv and mompS_alleles_ONTmompS.tsv in one file and confidence score.

[himamura2]

Dear Marit,
Thank you for crreating this tool, and this is not an issue but a request of a feature.

Now the tool creates two files

mompS_alleles_ONTmompS.tsv
Strain mompS1 mompS2
LEG1372_consensus 33 18
LpST_ONTmompS.tsv
Strain ST flaA pilE asd mip mompS proA neuA
LEG1372_consensus ST62 8 10 3 15 18 1 6

But clinicians want to these information in a single file like this
Strain ST flaA pilE asd mip mompS proA neuA mompS1 mompS2
LEG1372_consensus ST62 8 10 3 15 18 1 6 33 18

Is this possible to have this file as an option. Also they asked us that if the program can provide some kind of confidence score for the result.

In our testing, ONTmompS produced the correct typing for 12 samples using ONT de novo assembly by flye and medaka.
best,
Hideo

[marithetland]

Hi Hideo, apologies for the late response, I did not see this comment. Great to hear that the tool has worked for you. The terminal output does include mompS1 along with the other alleles and the derived ST, so you could store this as you run it. I will also add this as an optional output.

The confidence of calls are provided as descibed here: https://github.com/marithetland/ONTmompS?tab=readme-ov-file#output, where a call without any * means 100% sequence coverage and 0 SNPs.