Indexed Sequencing workflows with 5' to 3' directionality

Single-Indexed SequencingThe single-indexed sequencing workflow applies to all Illumina sequencing platforms, where an Index Read follows Read 1.

Dual-Indexed Workflow on a Paired-End Flow Cell

Forward Strand Workflow: MiniSeq with Rapid Reagent kits and the MiSeq.

Note: While MiniSeq Rapid reagents allow for dual indexing, Read 2 cannot be performed with the MiniSeq Rapid reagent kit.

Reverse Complement Workflow: iSeq 100, MiSeq i100 (read-first sequencing), MiniSeq with Standard reagent kits, NextSeq 500/550, NextSeq 1000/2000, NovaSeq 6000 with v1.5 reagent kits, and NovaSeq X Series.

For more information, see the Indexed Sequencing on Illumina Systems Guide.