The most convenient way to barcode a sample is the use of barcoded adapters, as depicted in the barcode design overview. One minor disadvantage is that the ligation might not be as efficient as with standard SMRTbell adapters, leaving some molecules only with one adapter. As barcoded adapter designs are inherently symmetric, we implemented ways to recover the demultiplexed yield from one-sided barcoded molecules with ease.
As the first step, generate HiFi data with ccs v6.3.0 or later. This version will store additional tags per records, indicating if the molecule has missing adapters on either side. The second step is to use the new
--hifi-preset SYMMETRIC-ADAPTERS introduced with lima v2.5.0, described here. That’s it.