What is the difference between a single and dual indexed library?

A single-indexed library has only 1 index, specifically in the p7-side adapter. This is called the i7 index and is sequenced during index read 1 of the sequencing run. A single-indexed library must have the index in the p7 adapter to sequence on Illumina instruments.

A dual-indexed library has 2 indexes, index1 (i7) in the p7-side adapter and index2 (i5) in the p5-side adapter. Dual-indexed libraries can either be combinatorial dual (CD) or unique dual (UD). This concept is explained in Understanding unique dual indexes (UDI) and associated library prep kits

Note: On Illumina instruments, it is not possible to sequence an i5 index without first sequencing the i7 index (ie, a single-indexed run only sequencing the i5 index is not possible).

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