I work in gram positives (S. aureus) and lately We have done WGS illumina single read for different clinical and lab strains. The results are really good. Also I had seen publication with illumina single read.
The problem is that we have to do WGS to some gram negatives (klebsiella and E.coli) and I had read that for this kind of bacteria is better Double read. I want to know if it true or we can also work with single reads (cheaper), and if it is better why (genome size?, amount of plasmids?)?
Thanks!!