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bvalot / pyMLST

whole genome MLST analysis
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Can't find allele #7

Open MMAThijssen opened 2 years ago

MMAThijssen commented 2 years ago

I have typed about a hundred samples using pyMLST. For a few samples, one of the alleles could not be decided. It always happened to be about the last gene in the scheme. I checked the contigs by aligning them with the reference and in all cases it could align, so it is not about missing data. Do you have any idea what could be the cause and how to resolve this?

bvalot commented 2 years ago

Hello,

I think the problem is for the MLST search. Can you give me which Species you look for and if you use assembly genome or raw read?

MMAThijssen commented 2 years ago

Hi, the issue is indeed with the cla MLST search. The species are Vibrio parahaemolyticus and Vibrio cholerae. The MLST was done on contigs.

bvalot commented 2 years ago

ok. How do you generate the database? With the "import" command?

MMAThijssen commented 2 years ago

I created the database with the create option

bvalot commented 2 years ago

Can you report me some results of the claMLST search and the log of the base creation?