Full-length adapters are compatible with ligation-based library construction workflows for direct and targeted multiplexed DNA and RNA (cDNA) sequencing applications on the Illumina® platform. Since sequencing barcodes are added during an adapter ligation step, full-length adapters are particularly well suited for PCR-free workflows.
KAPA Unique Dual-Indexed (UDI) and KAPA Dual-Indexed (DI) Adapters all have a standard Illumina adapter backbone. They are therefore easily incorporated in new and existing Illumina sequencing workflows, and do not require customized sequencing or indexing primers. A combination of 8-nt sequencing barcodes on each of the i5 and i7 adapter oligos supports paired-end sequencing on 2- and 4-channel Illumina instruments. KAPA UDI Adapters and KAPA DI Adapters both support a broad range of sample pooling (2- plex up to 96-plex, as appropriate for your workflow), for target enrichment and/or sequencing.
Your choice of unique vs. combinatorial dual-indexed adapters should be determined by your sequencing instrument and the sensitivity of your application to index misassignment. KAPA UDI Adapters employ 192 non-redundant barcodes for the 96 unique dual-index combinations, whereas KAPA DI Adapters offer a combinatorial approach (twelve i7 x eight i5 barcodes = 96 dual index combinations). Unique dual-indexing is recommended for all applications and Illumina sequencers, whereas combinatorial dual-indexing may suffice for older generation instruments with non-patterned flow cells.1,2
Refer to this table to determine whether KAPA UDI Adapters or KAPA DI Adapters are best for your application.