FAQ: Can the FFPE DNA Repair v2 Module repair damage in both single- and double-stranded DNA? Or, does it require double stranded DNA as a template? 

The full repair activity of the FFPE DNA Repair v2 Module requires dsDNA for polymerization and ligation. However, damaged bases such as dU present in ssDNA will be excised during repair and not be incorporated into the sequencing library.