Sequencing inDrop Libraries

Most users sequence their libraries on a NextSeq 75bp run:

Read 1: 61 
Read 2: 14
Index 1: 8
Index 2: 8

It is common to have 70-80% valid reads after filtering for valid cell barcodes.

Sequencing on a their libraries on a NovaSeq 100bp run:

Read 1: 86 
Read 2: 14
Index 1: 8
Index 2: 8

Our current experience with inDrops runs on a NovaSeq indicate that we are having some trouble on the Index reads. Some libraries are only getting 6 bp of the 8bp index read. This is leading to a lower percent of valid reads after filtering for valid barcodes 50-60%. Due to this, the NovaSeq seems most cost effective if sequencing with the full S1 or S2 flow cells.