subspecies determination errors

Question

subspecies determination errors

retimme opened this issue 5 years ago · comments

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

Arjun Prasad · Answer 1 · Wed Aug 05 2020 23:56:06 GMT+0800 (China Standard Time)

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).