Question Regarding Adapter Detection with fastp and Trimming with Trimmomatic

mahsa · February 20, 2026, 1:46pm

Is it methodologically appropriate to use fastp only for adapter detection and then perform the actual adapter trimming using Trimmomatic?
In other words, is it acceptable to identify the adapter sequences with fastp first and subsequently provide those sequences to Trimmomatic for precise adapter removal, or would it be more appropriate to use a single tool for both detection and trimming?

Evangelos_Karatzas · February 23, 2026, 8:40am

I don’t see any reason why that wouldn’t be valid, but!

First I would do both the things you suggested (finding adapters with fastp and then 1. remove them with fastp and 2. remove them with trimmomatic). Then benchmark the biological results -they should be the same more or less; if they are not, go with the tool that makes more sense. If they are similar, go with the fastest tool (time benchmark). But I guess the overhead of switching from 1 tool, to 2 tools probably leans the scale towards just using fastp.

TLDR; Benchmark results quality and execution times and go with what makes more sense

Evangelos_Karatzas · February 23, 2026, 8:41am

Now if you want a list and examples of various adapter removal and merge tools already in nf-core to use for your cases, have a look into the tools offered by this subworkflow:

github.com/nf-core/modules

subworkflows/nf-core/fastq_removeadapters_merge/main.nf

fdcc3976e

// both SE and PE
include { TRIMMOMATIC                         } from '../../../modules/nf-core/trimmomatic/main'
include { CUTADAPT                            } from '../../../modules/nf-core/cutadapt/main'
include { TRIMGALORE                          } from '../../../modules/nf-core/trimgalore/main'
include { BBMAP_BBDUK                         } from '../../../modules/nf-core/bbmap/bbduk/main'
include { LEEHOM                              } from '../../../modules/nf-core/leehom/main'
// both SE and PE, plus merging
include { FASTP                               } from '../../../modules/nf-core/fastp/main'
include { ADAPTERREMOVAL as ADAPTERREMOVAL_SE } from '../../../modules/nf-core/adapterremoval/main'
include { ADAPTERREMOVAL as ADAPTERREMOVAL_PE } from '../../../modules/nf-core/adapterremoval/main'
// helper module for concatenating adapterremoval paired-end processed reads
include { CAT_FASTQ                           } from '../../../modules/nf-core/cat/fastq/main'

workflow FASTQ_REMOVEADAPTERS_MERGE {

    take:
    ch_input_reads                 // channel: [mandatory] meta, reads
    val_adapter_tool               // string:  [mandatory] tool_name // choose from: ["trimmomatic", "cutadapt", "trimgalore", "bbduk", "leehom", "fastp", "adapterremoval"]
    ch_custom_adapters_file        // channel: [optional]  {fasta,txt} // fasta, for bbduk or fastp, or txt, for adapterremoval
    val_save_merged                // boolean: [mandatory] if true, will return the merged reads instead, for fastp and adapterremoval

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Question Regarding Adapter Detection with fastp and Trimming with Trimmomatic

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