question about illumina adapter sequences

Question

[Meghan.T]

Hi guys

I got my hands on a data sequenced with NovaSeq 6000 . It is a little silly but I am not sure what sequences to use for adapter trimming. The pamphlet of Illumina (https://thesequencingcenter.com/wp-content/uploads/2021/12/illumina-adapter-sequences.pdf) does not exactly specify what the forward and reverse sequences of adapters are for Novaseq 6000. Can anyone guide me through this?

Answer 1

[GenoMax]

Adapters are not specific to the sequencer they are generally library kit specific. You can use a program like fastp to recognize and trim the adapters automatically. You can also use bbduk.sh from BBMap package. BBMap includes an adapters.fa file that has many standard adapters used for Illumina libraries.

[Meghan.T]

Oh! thank you very much! They stated that they used KAPA Hyper Prep Kit to construct the library. so I have to search for adapter sequences of this kit?