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Issues with the allele call using chewbbaca for cgMLST

I was exploring the chewbbaca, and I found that I had many alleles which were truncated versions of the a different allele, but was assigned novel allele number. I used the default allelic length variation of 20% from modal length, and all the truncated alleles had length larger than 80% of the full length gene. How can I adapt the scheme for establishment in PubMLST, which is more conservative?

cgmlst allele chewbbaca calling

1 answer

Hi,

In my experience, it really helps providing species-specific prodigal training files. Some of those are linked here.

For external schemes, you can use the PrepExternalSchema function. The result can be used in the AlleleCall step.

Cheers,

Michael

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