This documentation lists the adapter sequences for Illumina library prep kits.
For product compatibility information, visit the support pages for your library prep kit on the Illumina website (support.illumina.com).
Dual indexing on the following instruments requires the reverse complement of the Index 2 (i5) adapter sequence: iSeq 100, NovaSeq 6000 with v1.5 reagent kits, MiniSeq, NextSeq 2000 in Standalone mode, NextSeq 550, NextSeq 500, HiSeq 4000, HiSeq 3000, and HiSeq X Systems.
|•||If you are manually creating a sample sheet for these systems, enter the reverse complement of the sequence.|
|•||If you are using Instrument Run Setup, Sample Sheet Manager (SSM) (SSM), Analysis Software (AS) Prep tab, or Local Analysis Software to record the adapter sequences, the software automatically creates the reverse complement.|
|•||NextSeq 2000 uses an in-solution primer for Index 2. However, the DRAGEN on-instrument platform will automatically reverse complement i5 indexes during secondary analysis.|
|–||If you are using Instrument Run Setup or manually creating a sample sheet in v2 file format, enter the forward orientation of the sequence.|
|–||If you are manually creating a sample sheet in v1 file format, enter the reverse complement of the sequence.|
Sections for kits that recommend adapter trimming include the adapter trimming sequences. The adapter sequence is the sequence of the adapter to be trimmed.
When read length exceeds DNA insert size, a run can sequence beyond the DNA insert and read bases from the sequencing adapter. To prevent these bases from appearing in FASTQ files, the adapter sequence is trimmed from the 3′ ends of reads. Trimming the adapter sequence improves alignment accuracy and performance in Illumina FASTQ generation pipelines.
SSM, Instrument Run Setup, Analysis Software (AS) Prep tab, and Local Analysis Software record adapter trimming sequences for Illumina kits in the sample sheet. For specific settings, see the documentation for your software. Instrument Run Setup is documented in the NextSeq 2000 Sequencing System Guide (document # 1000000109376).