casava 1.8.2 adapter masking new option

[riv]

Hello,

I am starting to work with casava 1.8.2 for demultiplexing data with samples with dual and single index in the same paired-end Illumina flow cell.

I found this new option of casava --adapter-sequence in which you can give a fasta file in order to mask the adapters.

Does anybody use this adapter masking option already? Does it work Ok for multiplexed-dual index data?

Thanks for the feedback!