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?
• 84 views
•
link
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
• 0 views
•
link
Log in to answer this question.