When performing sequencing on an Illumina instrument, sequences corresponding to the library adapter can be present in the FASTQ files at the 3’ end of the reads if the read length is greater 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 both BaseSpace Sequence Hub Prep tab and Local Run Manager have adapter information built in. 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.
TruSeq LT and TruSeq HT-based kits:
ScriptSeq and TruSeq DNA Methylation:
TruSeq Small RNA:
TruSeq Ribo Profile:
AmpliSeq, Nextera, Nextera DNA Flex, Nextera DNA, Nextera XT, Nextera Enrichment, Nextera Rapid Capture Enrichment, TruSight Enrichment, TruSight Rapid Capture Enrichment, TruSight HLA:
Nextera Mate Pair: