Application of chewBBACA onto Fungal Genomes

[maurkarr]

Hello,

Wondering if the tool would be suitable for creating a cgmlst scheme for fungal species such as those within the Aspergillus nigri section (haploid). I have followed the tutorial using aspergillus, which did produce results. I am wondering if there are any pitfalls in the way the chewbbaca tool operates that would not allow this scheme to be used to make any sort of meaningful conclusions about the way my isolates cluster based on cgmlst.

[rfm-targa]

Dear @maurkarr,

Thank you for your interest. We have not tested chewBBACA with fungal species. chewBBACA uses Prodigal/Pyrodigal to predict ORFs, which were designed to work with bacterial genomes. It might work with haploid species with single exon genes. One way to test that is to run Prodigal/Pyrodigal and validate the predicted coding sequences (CDSs) against the annotated CDSs in a reference genome. You can also run chewBBACA and compare the schema loci with the annotated CDSs in the reference genome. To do that, you should create a Prodigal training file based on the reference genome, using the genetic code used by the species, and simply pass the reference genome to create a schema. If the schema loci match the annotated CDSs, you might be able to use the schema for allele calling and get useful results.
It is an interesting application, and different from what chewBBACA was designed for. Please let us know if it works.

Kind regards,

Rafael

[dutchscientist]

I am working on this, see #211. It is possible, but it may have problems with genes containing introns (i.e. like in Aspergillus).