Adapter trimming WGS Illumina DNA PCR free kit with BBduk

Question

[omicsfury]

Dear All,

I'm starting the analysis of WGS data prepared with Illumina DNA PCR free kit. I want to remove adapters using BBduk tool. To do that I want to provide adapter sequence in my fasta file. I am confused how should I text the adapter sequence to my fasta file. The adapter sequence in the sample sheet is separated by "plus" sign:

AdapterRead1    CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA
AdapterRead2    CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA

Should I paste the sequence to the fasta file as it is with "plus" sign, or should I remove the sign?

Please help and explain if possible.

Regards!

Answer 1

[GenoMax]

You should provide them separately as two sequences in the adapter file.

Illumina says the following for DNA PCR-free tagmentation adapters :

The following sequence includes two adapter sequences joined by a plus sign. When performing adapter trimming, the software independently assesses each adapter for trimming.

CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA

[omicsfury]

Thank you so much!