No, the NEBNext Ultra II FS DNA Module is not compatible with bisulfite conversion or EM-seq workflows. We recommend you use either NEBNext UltraShear™ (NEB #M7634) or mechanical shearing, followed by the NEBNext Ultra II DNA End Repair/dA-Tailing Module (NEB #E7546) for this application. After fragmentation with NEBNext UltraShear, you can go straight into End Repair/dA-Tailing reaction as described in section 2 of NEBNext UltraShear manual without a cleanup.
