Generally, for Illumina sequencers, you can use different sets of indexes in the same run if they have the same length. Indeed, you may be able to multiplex, in the same run, libraries obtained using our Bundle Solutions and libraries performed with other kits as long as they use: 

– non redundant index sequence of 8bp

– standard sequencing primers from Illumina

Moreover, when sequencing libraries are generated with Bundle Solutions from SOPHiA GENETICS,  the complexity of sequencing parameters is reduced, thus enabling  multiplexing with other kits in all Illumina instruments.

On the MiniSeqTM, however, simultaneous analysis of both kits is not possible. In this case, you can still sequence the samples together, but you need to perform the analysis twice. You can start by analyzing the samples from the other commercial kit and then re-import the run into a new analysis once the first has completed.