Prepare Reference Files
The reference files required for making the MappingConfig file is listed below

Reference FASTA

I download reference FASTA from the UCSC genome browser. For mapping, I will keep all the small contigs to make sure all reads mapped properly, but I usually remove them and only focus on the main chromosomes for further analysis.
Another thing is the lambda DNA spike-in as a non-conversion estimation (we do that), I usually append the lambda genome with the name chrL to my genome FASTA. You can download the chrL from NCBI and append that to your genome.

Bismark Reference

Use bismark to prepare the genome index, see its documentation here. Note that we use bowtie2 for snmC-seq and snmCT-seq (that's bismark's default also), and bowtie1 for snm3C-seq (the same as snm3C-seq paper).

Gene Annotation GTF (mct only)

For human and mouse, we usually use GENCODE's latest version. But I do not update GTF throughout the same project. (And the difference between versions probably have little impact on your analysis results.)

STAR Reference (mct only)

Use STAR to prepare its genome index, see its documentation here.