Illumina DNA Prep with Enrichment Compatible Products

Sample Information

Before preparing libraries, record information about your samples using an option available for your sequencing system.

• iSeq 100 System
• MiniSeq System
• MiSeq System
• NextSeq 500 or NextSeq 550 Systems
• NextSeq 2000 System
• NovaSeq 6000 System
• HiSeq Series—Use Illumina Experiment Manager to record samples

Library Prep

Index Kit

Illumina DNA Prep with Enrichment is compatible with IDT for Illumina DNA/RNA UD Indexes.

FFPE Input

To start the protocol from extracted FFPE, use the Infinium FFPE QC Kit for FFPE qualification. For instructions, see the Infinium FFPE QC Assay Insert.

Sequencing Guidelines

IDT for Illumina DNA/RNA UD Indexes

Illumina recommends setting up a paired-end run with 101 cycles per read (2 x101) and 10 cycles per index read, regardless of the enrichment probe panel you are using. If you would like additional overlapped reads or raw coverage, you can sequence up to 2 x 126 or 2 x 151, but it is not required.

If setting up a 2x151 sequencing run for additional overlapped reads or raw coverage, see the following table.

For the MiniSeq and NextSeq 500/550 Systems, the reagent cartride RFIDs encode a maximum number of cycles. The maximum value in the 300-cycle kit does not allow the full read length for Read 1 and Read 2 when each Index Read requires 10 cycles. Therefore, sequencing the full read length requires subtracting two cycles each from Read 1 and Read 2.