Which barcodes should be used for multiplexing ?

In general, we recommend processing a minimum of 8 samples, using a complete set of eight 6 nt i7 indices for multiplexing (e.g., 7001 - 7008). However, if fewer barcodes are required, care should be taken to always use indices which give a well balanced signal in both lasers (red and green channels) for each nucleotide position.

All columns (1-12) and rows (A-H) of the 6 nt indices (7001 – 7096) fulfill these criteria. The individual libraries within a lane should be mixed at an equimolar ratio to ensure this balance.

An Index Balance Checker tool to  select the optimal index combination for multiplexed sequencing of index subsets is available under Support Tools.