stajichlab/PopGenomics_Clusitaniae: v1.0.0 dataset to support Murante et al study

This release is a freeze of dataset and analysis scripts to explore variation in genomes of strains from CF patients, environmental set, and public SRA strain sets. The population genomic pipeline for genotyping Clavispora (Candida) lusitaniae populations. The pipelines for generating SNP and INDEL genotypes in VCF format along with CNV visualization, capturing unmapped reads to look for novel haplotypes, generate strain phylogenetic trees, and compare SNP and INDEL impacts on predicted genes to prioritize functional mutations. The analyses also examine Pooled strain collection to estimate allele frequencies within a population.