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denglab / SeqSero2

SeqSero2
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subspecies determination errors #27

Closed retimme closed 3 years ago

retimme commented 4 years ago

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

evolarjun commented 4 years ago

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).