I'm working on a phylogeny of Salmonella subsp. arizonae and have located a few subsp. determination errors in SeqSero2:
SRR1175814 - SeqSero2 determines IIIa, but actually I
SRR4297729 - SeqSero2 determines IV, but actually IIIa
SRR3418287 - SeqSero2 determines II, but actually IIIa
Not sure what mode you're running SalmID in, but in the miniassembler mode I think the subspecies is determined by SalmID (https://github.com/hcdenbakker/SalmID).
I'm working on a phylogeny of Salmonella subsp. arizonae and have located a few subsp. determination errors in SeqSero2:
SRR1175814 - SeqSero2 determines IIIa, but actually I SRR4297729 - SeqSero2 determines IV, but actually IIIa SRR3418287 - SeqSero2 determines II, but actually IIIa
Attaching the phylogeny, highlighting these tips. core_gene_FastTree_191112.pdf
Thanks for the great work on this program! -Ruth