Sequence bacterial genome and amplicons on the same run

[F.Lazaro]

Hello everyone,

At the moment we are using Miseq to sequence both bacterial and viral genomes at very low throughput. I would like to know if there could be any problem in sequencing these very different genomes on the same run (5mb vs 5 kb).

Thanks!

PD: I meant viral genomes not amplicons

[thermophile]

As long as they are roughly the same sheared size, this will work well. Total size of the genome doesn't effect the run quality, you just need to account for it when deciding how much of each genome to pool

[Genetic Librarian]

Hi,

as long as you index each sample individually this should be no problem.
Just take care that both libraries end up having a similar fragment size. Smaller libraries cluster preferentially, so if your genomes are at 500 bp and your viromes at 300 bp and you mix them 70/30, your read output would be closer to 50/50.

[F.Lazaro]

Thanks!

That was my intention. To shear both genomes to almost the same fragment size and indexing each sample.
Regarding the proportion of bacterial genomes and viromes, is there any way to predict the outcome?(Number of bacterial genomes and viromes might be different each time)

[Genetic Librarian]

Sure, all you need is your genome sizes and the desired coverage and you can calculate how many % of a run is needed per sample.
You can check out the Illumina Coverage Calculator for that.