Technical data

5 Indexing and Sample Processing for Multiplexed Sequencing

Guidelines for sequencing sample preparation and run setup

86 SureSelect

Target Enrichment System for Illumina Multiplexed Sequencing

Guidelines for sequencing sample preparation and run setup

Use the appropriate Illumina Paired-End Cluster Generation Kit to do

cluster amplification.

Refer to the instructions that are included with the Illumina Paired-End

Cluster Generation Kit. The optimal seeding concentration for SureSelect

libraries is 6 to 8 pM, depending on the desired output and data quality.

Sequencing run setup guidelines for 8-bp indexes

For libraries prepared using kits with 8-bp indexes, sequencing runs must

be set up to perform an 8-bp index read. For the HiSeq platform, use the

Cycles settings shown in Table 46. Cycle number settings can be specified

on the Run Configuration screen of the instrument control software

interface after choosing Custom from the index type selection buttons.

For complete 8-bp index sequence information, see Table 52 on page 92.

Table 46 HiSeq platform Run Configuration screen Cycle Number settings

* Settings apply to v3.0 SBS chemistry.

Run Segment Cycle Number

Index 1 (i7) 9

Index 2 (i5) 0