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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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Fungal genomes not working #121

Open 14corman opened 2 years ago

14corman commented 2 years ago

Hello,

We have been using this MLST tool for many years now, but have not updated it until recently. We were using version 2.9 up till recently which would result ST for fungal. We updated to 2.19 and noticed Fungal schemes were removed and we were not getting ST results for fungal isolates. After some digging, we noticed that those schemes are removed from the provided pubmlst, so we rebuilt that database while adding these schemes back in.

We then tried a 'cglabrata' isolate and it returns no ST result. If we try the same isolate in the 2.9 version, we get the correct result.

Would someone be say what has changed in MLST to need removal of the fungal schemes since they may not be working anymore? I cannot see any documentation other than the release notes saying that fungal schemes are removed. Any information would be helpful.

Thank you

14corman commented 2 years ago

I just noticed that it says on the main README that only MLST schemes with less than 10 genes are included. Is that the reason for the removal of fungal isolates?