Sequencing primer compatibility and recommended library kits for the HiSeq 1000/2000 and 1500/2500

Illumina offers a wide array of library preparation kits and sequencing platforms for different applications, each with its own coverage and indexing considerations. Table 1. and Table 2. list the sequencing primers included in the HiSeq 1000/2000 and 1500/2500 cluster kits, and include the Illumina library preparation kits compatible with the HiSeq 1000/2000 and 1500/2500 platforms based on the required data output and the indexing capabilities of each kit.

Note: The information in the tables below is based on the required data output and indexing capabilities of each kit. Most Illumina libraries can be sequenced with all Illumina sequencing platforms. If a specific Illumina library is not listed below, contact Illumina Tech Support to discuss special considerations.

Refer to the Sequence Coverage Calculator and Library Prep and Array Kit Selector resources for additional information.

Table 1. Sequencing primer compatibility on the HiSeq v4 high output chemistry based on recommended library type and flow cell type.

Table 2. Sequencing primer compatibility on the HiSeq v3 high output chemistry based on recommended library type and flow cell type.

\* Any dual indexed library that is sequenced on a single read flow cell requires the TruSeq Dual Index Sequencing Primers - Single-Read (FC-121-1003), which supplies HP9. \\ These library kits require primers from the TruSeq Dual Index Sequencing Primer Box. TruSeq Dual Index Sequencing Primers - Single-Read (FC-121-1003): contains HP10 (Read 1), HP12 (index i7), and HP9 (index i5) TruSeq Dual Index Sequencing Primers - Paired-End (PE-121-1003): contains HP10 (Read 1), HP11 (Read 2), and HP12 (index i7)

Table 3. Sequencing primer compatibility on the HiSeq rapid v2 chemistry based on recommended library type and flow cell type.

For instructions on how to use custom primers on the HiSeq 1000/2000 and 1500/2500 sequencing platforms, refer to the following resources:

• Spiking custom primers into the Illumina sequencing primers

• HiSeq System Custom Primers Guide

For any feedback or questions regarding this article (Illumina Knowledge Article #1491), contact Illumina Technical Support [e-mail].