How to find adapter sequences for trimmomatic

Question

[wonde2000]

I am new to bioinformatics and I downloaded Illumina Hiseq 2000 DNA sequence data from NCBI. Now, I am planning to trim adapters ( make quality control) using trimmomatic 0.39. is there anyone who would provide me adapter sequence for the stated platform in a fasta format? Thank you in advance for your help.

Answer 1

[ATpoint]

The adapter depends on the library preparation kit, not the sequencing machine. Run fastqc to see if you even have any adapter contamination. It will tell you the name of the adapter if there is any, and then you can google that. Most of the time it is the standard Illumina TruSeq or Nextera adapter, sequences are online, for example at Illumina: https://support.illumina.com/downloads/illumina-adapter-sequences-document-1000000002694.html