I've been working with higher model organisms so far (mouse/human). Now I'd like to analyse non-model yeasts. I don't see an issue with using my standard analysis workflow for this organism as well:
Genome analysis: bwa-mem & GATK (although I need known SNPs for GATK - is there a better tool to call SNPs in yeast?)
Transcriptome analysis: STAR, featureCounts & voom/Limma
However, is there anything I should watch out for and how would you recommend performing pathway analyses? Maybe using KOBAS? Any advice is highly appreciated.