Is it possible to create a single, mixed sequencing run containing samples prepared with different kits (e.g. a Bundle Solution by SOPHiA GENETICS + samples prepared with other commercial kits)?
It may be possible to multiplex samples in the same run if the following conditions are met:
1) Using an index length of 8bp
2) Using standard Illumina sequencing primers
3) Using a MiSeq™, NextSeq™ or HiSeq®
For the MiniSeq™ platform, simultaneous analysis on both kits is not possible. In this case, samples can still be sequenced together but will require separate analysis. This can be accomplished by analysing the samples from the other commercial kit first and then re-importing the run into a new analysis once the first has completed.