The three sheets of the following Google Sheets Docs contains all the primer files used.
The design for this pilot experiment included 96 well oligos that acted as the i7 index, and plate primers that acted as the i5 index. In this database there are three sets of indexed oligos: one for each of our SARS_CoV-2 target designs (N1, S2) and one for RPP30. At Octant, we have used lots of different paired barcoded designs. For clinical work, and to avoid any issues regarding barcode mixing, one might want to order unique i5 and i7 for each sequence.
Note: At Octant, we have found over the years that there is an idiosyncrasy with certain barcodes that drop out of sequencing runs routinely. We have never found a way to predict this ahead of time, and it is usually easiest to run positive controls on each new barcode that is used.
The amplicon files for the SARS CoV-2 targets (N1, S2), their corresponding synthetic spikes, and the RRP30 amplicon are listed below. All relevant sequencing primers are annotated.
s2_synthetic_spike-in_amplicon.gb