I am so excitied to see this paper Comparing genomic variant identification protocols for Candida auris, led by Christina A. Cuomo and Anastasia P. Litvintseva, being published.
With Ferry Hagen, we contributed a pipeline to this study that is available at my github: https://github.com/vuthuyduong/SNPanalysis. This pipeline can be used for Illumina, PacBio, and Nanopore reads.