MISEQ: Mixing Amplicon with Resequencing samples

[docsascha]

Dear All,

Another question from the newbie.

Does anybody know if it is possible to mix Samples for Amplicon Sequencing and genome resequencing?
We are a small lab and just have to do few Amplicon Sequences a month, main task at the moment is resequencing for outbreak investigation. So it would be great to mix samples, and we could save on PhiX spiking
Methods used at the Moment
V3 Kits
Nextera library Prep
Miseq System


Alexander

[bunce]

Hi docsascha, Yes we have blended shotgun data and amplicon together in one run. Getting a decent library blend and quant can be challenging... but it is certainly possible. Ultimately it comes down to being confident that the indexing you are using can differentiate the a samples. We still put PhiX in all runs at 5-10%. Cheers Mike