How to remove nextera with fastp

Question

[Mat]

When run Fastp with

fastp -i in.R1.fastq.gz -o out.R1.fastq.gz -I in.R2.fastq.gz -O out.R2.fastq.gz --detect_adapter_for_pe --disable_quality_filtering --length_required 15

Fastq still detects nextera transposase sequences in the output. Is there a way to remove them with Fastp?

Answer 1

[Istvan Albert]

Explicitly specify your adapters. Create the adapter file

>nextera
CTGTCTCTTATACACATCTCCGAGCCCACGAGAC

now use the file with the -a flag.