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

frossit · 10-14-2016, 07:54 AM

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 · 10-14-2016, 07:34 PM

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

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10-14-2016, 07:54 AM	#1
frossit Member Location: Brasil Join Date: Jun 2011 Posts: 12	Sequencing Ninblegen and Nextera libraries in the same lane in a Miseq 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 Last edited by frossit; 10-14-2016 at 07:58 AM.

10-14-2016, 07:34 PM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	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