Question: Is the genome application strand-specific DNA sequencing?
Answer: The genome application is not stranded. The denaturating agent (step 2.2 of the user guide) makes all DNA input single-stranded. These single-stranded molecules get partitioned at random throughout all the GEMs and the isothermal amplification on the GEMs will amplify all molecules, regardless of strand identity.
Separation of the two haplotypes (maternal vs paternal) occurs upon identification of SNVs and phasing of the variants.