Hi all..
I am seeking advice on the preferred method for sequencing a bacterial 16S metagenome: Illumina platform or Nanopore method? Any insights or experiences would be appreciated. #sequencing #metagenomics #researchmethods
16S V1-V2 or V4 regions: Illumina 2 X 250
16S V3-V4 regions: Illumina 2 X 300.
Nanopore can produce longer reads, but due to a higher error rate, it doesn't have any advantage compared to Illumina if the whole community is targeted.
Nanopore has an advantage when you want to use whole genome metagenome sequencing. The standard 16S metabarcoding is done by illumina, but nanopore can be used if you want to sequence the whole 16S gene.
the choice of which primers to use and the region to sequence also depends on the environment that you are testing. It is always advisable to do a PCR+Gel before you decide on the primers and send the DNA for sequencing, just to see that your choice is suitable for your data. In my experience not all primers work equally good in all environments.
- Badges
- Science topic