...
Data analysis with breseq (like all other programs) is only as good as the data that goes into it. The MultiQC and Trimmomatic tutorials work well upstream of breseq, while the identification of novel DNA elements may be useful for things such as trying to identify unknown plasmids and makes use of the genome assembly tutorial.
Alternatively, again consider going back to the intro breseq tutorial to rerun the sample that you took through read QC, mapping, SNV calling, and visualization.