Hello, for regular DNA processing (https://ccb.jhu.edu/software/centrifuge/), we can use Centrifuge or similar tools to classify which organism a fragment of DNA belongs to, using metagenomic indices.

I am currently dealing with data that has been subjected to bisulfite treatment, therefore unmethylated cytosines appear as thymine when sequencing. Does anybody know of metagenomic classifiers that deal with bisulfite treated DNA? For example, for aligning we can use Bismark instead of tools like Bowtie. Is there something that can classify as well?

Thank you