I have obtained several hundred raw, unassembled yeast genomes from NCBI and I am looking for advice on how to process the genomes for downstream analysis.
I have a reference genome (S288C) to use for assembly/alignment but I'm not sure what to do first.
So far I have run a quality assessment (FastQC) followed by trimming (Trimmomatic). But I'm not sure if I should align or assemble next. The problem with yeast is if I assemble to a reference genome it reduces the genome to a haplotype and could miss moments of heterozygosity present. And I'm not sure how it would work to do a de novo assembly as I'm assuming it's the same problem. Same with aligning to the reference genome.
Are there ways to work around this? Does the yeast research community just ignore this issue? Are there tools currently out there that take all of this into account?