I have done genome assembly for various yeast strains in pseudochromosome level. All of them was treated exactly the same way. I don't understand why one of them is more fragmented than others. The sequenced data were created using Illumina short-read and Nextera library. FastQC returned errors in "per base sequence content" and "sequence duplication levels" for all strains except this fragmented one (warning). Do you have any suggestion why this assembly could be more fragmented than others?
Any suggestions or help would be much appreciated.