High throughput amplicon sequencing

One of the features of high throughput sequencers is the possibility to mix libraries of different origin/samples in the same run. Library multiplexing/de-multiplexing uses index sequences that are incorporated into the adapters used to create the sequence library. The number of indexes is virtually unlimited.

As a result, amplicon sequencing, even when the total target size is small, can profit from the capacity of high throughput sequencers by combing the same amplicons from hundreds to thousands of samples. Illumina type sequencing amplicons are typically 100 to 2000bp, and a maximum of 600 bp of these amplicons ca be sequenced.

Oxford Nanopore allows also Long Range -PCR amplicons to be sequenced directely. Oxford Nanopore has typically a higher sequencing error rate than Illumina sequencing.