choosing between sistr prediction and refseq match

phac-nml / sistr_cmd

SISTR (Salmonella In Silico Typing Resource) command-line tool

Apache License 2.0

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choosing between sistr prediction and refseq match #50

Open vappiah opened 3 years ago

vappiah commented 3 years ago

Dear Developers,

We recently used sistr to serotype some salmonella samples. We realized that the Sistr serovar overall prediction is different from the RefSeq match. In such instances, which serovar do I choose?

Please advice. Thanks

kbessonov1984 commented 3 years ago

Hello, the SISTR serovar overall filed is considered to be the final result as it takes into account both RefSeq, MLST and Alleles fields predictions. The discrepancy could be due to high degree of similarity between serovars or sample quality issues. Please also check that alleles found and alleles matched fields are close to 330 value. Thank you for reporting your concern