I have WGS data (2x150b paired end NextSeq reads) for Yeast (sacCer3) and would like to know how much coverage the data has relative to the reference genome.
My plan here is to use STAR to align the dataset to the reference (sacCer3), and then Qualimap to analyze the resultant BAM file.
Is STAR the right alignment tool to use for yeast WGS data? Or is STAR better suited to RNA-Seq data ... and so I should be using a tool like BWA-Mem?
Does the choice of tool matter if the dataset was from mouse, rat, or human as opposed to yeast?