Where are the illumina adapters on Trimmomatic take from?

Question

[bioinfo]

Hello,

I am looking into trimmomatic to trim the adapters in my data.

Illumina says that for the kit that I used the sequence that I need to specify for adapter trimming for both R1 and R2 is: CTGTCTCTTATACACATCT (https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Nextera/SequencesNextera_Illumina.htm)

I was thinking of using the ILLUMINACLIP:NexteraPE-PE parameter of trimmomatic. However, when I look at the github https://github.com/timflutre/trimmomatic/blob/master/adapters/NexteraPE-PE.fa the sequences are slightly different.

>Trans1_rc
**CTGTCTCTTATACACATCT**GACGCTGCCGACGA

>Trans2_rc
**CTGTCTCTTATACACATCT**CCGAGCCCACGAGAC

It does seem to be that the sequence shown in the illumina documentation is part of the one included in trimmomatic but there are additional bases in the one from trimmomatic. Which one is more correct to use? I cannot figure out where the additional bases come from.

Thank you

Answer 1

[GenoMax]

Illumina indexed adapters share a core sequence at the beginning which is what is indicated in your link. Trimming programs will remove sequence (including the adapter and everything to 3' of that) once they find this core sequence in the data. You can specify the sequence you need instead of using bundled files.

[bioinfo]

Thank you for the explanation. Is it more appropriate then to use the sequence from the illumina documentation or the one from the github?

[GenoMax]

Use the sequence Illumina recommends for the specific kit.