Sequencing Ninblegen and Nextera libraries in the same lane in a Miseq

[frossit]

Hi !
We want to sequence 12 plasmids. 10 libraries were constructed using Ninblegen Seq Cap EZ Library SR (single index) and 2 using Nextera (dual index). We are planning to pool all these libraries and performing sequencing using a MiSeq Nano Kit v2 flowcell. Could I sequence libraries constructed using kits from different manufactors in a single lane ?
Thanks

[nucacidhunter]

You can, but note following:

1- Libraries with shorter insert size will sequence more efficiently so you have to load more from larger libraries if you want relatively equal number of reads

2- Index read and demultiplexing: if your Nextera libraries index 1 are different then you can do only one index read otherwise you have to do two index reads. I am not sure if you can mask the index 2 for libraries with only one index with MiSeq software but it can be done with bcl2fastq