Allele workflow issue: correct identification of antigen but erroneous prediction of serotype

[GuilhemRoyer]

Hi,

First of all, thank you for this great tool! I have used the different workflows available and have encountered problems with the "Allele workflow". When I look at the SeqSero_log I have found matches with O-4, fljB 1,2 and fliC i. However, the predicted antigenic profil result is "1,3,19:i:1,2" the predicted serotype is "Stratford".

Using the "Raw reads kmer" and "Genome assembly kmer" workflows I have no problem and have obtained obtained the correct profil (i.e. "4:i:1,2") and serotype (i.e. "Typhimurium").

I've had this issue with two different strains of Salmonella serotype Typhimurium...

Do you have any ideas to explain these differences?

Best,

Guilhem