When performing sequencing on an Illumina instrument, sequences corresponding to the library adapters can be present in the FASTQ files at the 3’ end of the reads if the read length is longer than the insert size. To remove these sequences and prevent issues with downstream alignment, adapter trimming is an option in Illumina FASTQ generation pipelines. Sample sheets generated with Illumina Experiment Manager contain the necessary sequences in the Settings section for Illumina kits. Illumina kits in BaseSpace Sequence Hub Prep, BaseSpace Sequence Hub Instrument Run Setup, and Local Run Manager have adapter information built into the software. However, some third-party tools require the adapter sequence for trimming be specified separately. The recommended sequences to use for each Illumina kit are as follows.
Note: if only one sequence is listed, that sequence is used for both reads of a paired-end run. Where the sequence differs between Read 1 and Read 2 of a paired end run, the sequence for each read is listed.
TruSeq single index (previously LT) and TruSeq CD index (previously HT)-based kits:
AmpliSeq for Illumina; Illumina DNA Prep (M) Tagmentation (previously Nextera DNA Flex); Illumina DNA Prep with Enrichment (S) Tagmentation (previously Nextera Flex for Enrichment); Nextera DNA; Nextera XT; Nextera Enrichment; Nextera Rapid Capture Enrichment; TruSight Enrichment; TruSight Rapid Capture Enrichment; TruSight HLA; Illumina Stranded mRNA Prep, Ligation; Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus; Illumina RNA Prep with Enrichment, Ligation:
Illumina DNA PCR-Free Prep, Tagmentation
ScriptSeq and TruSeq DNA Methylation:
TruSeq Small RNA:
Nextera Mate Pair: