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?
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