Agilent SureSelect V5 adapters for WES

Question

[Rick P]

Hi all,

I have raw paired-end WES FASTQ files whose library was prepared using the Agilent SureSelect Human All exon V5 kit.

After submission to FASTQC, all files showed a high percentage of reads with Illumina Universal adapter. However, for the purpose of quality trimming of raw reads using Trimmomatic, I need to know the sequence of these adapters.

The adapter sequences provided on the Trimmomatic package do not appear to include the SureSelect adapaters. Or, as we are talking about Illumina Universal Adapters, do I need to look for elsewhere? Where can I find the information about these adapters?

Thanks.

Answer 1

[GenoMax]

Looks like Agilent makes a tool available AGeNT (LINK) for trimming. I think these are just standard TruSeq adapters. So trimmomatic, bbduk.sh or fastp can all be used.

[Rick P]

Thanks! I will give it a try.

Although I think I might have found the correct sequence for the Illumina Universal adapter: it begins with AGATCGGAAGAG