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Updated Oct 19, 2026

Utilities

Trim FASTQ reads and collect fastp quality reports

fastp-qc is an offline FASTQ quality-control and adapter-trimming node.

Agent
Trim paired adaptersRemove low-quality readsRetain QC evidence

overview

What fastp-qc does

Quality-control and trim FASTQ reads (single or paired end) with fastp. Adapters are auto-detected and trimmed, low-quality and N-rich reads filtered; returns trimmed reads, native JSON/HTML reports and a summary.

Process single-end or paired-end FASTQ with fixed fastp defaults, quality and N filtering, a 15-base minimum length and two worker threads. Paired reads use overlap-based adapter detection. The output folder contains trimmed_R1.fastq.gz, optional trimmed_R2.fastq.gz, native fastp.json and fastp.html, fastp.log and a summary.json.

Supply a folder and relative read1 filename; read2 is optional. Files may use .fastq or .fq, optionally gzip-compressed, with a 4 GiB limit per input. The node exposes no trimming-parameter ports. Input yielding no valid reads fails instead of returning an empty success.

Packaged version: 1.3.7. Upstream license: MIT.

source github.com/OpenGene/fastp/tree/8a2397b6628ae14127efdb7566f67fc05f9aea56

use cases

Where fastp-qc fits

Trim paired adapters

Process matching read1 and read2 FASTQ files together.

Remove low-quality reads

Apply the packaged quality and N filtering defaults.

Retain QC evidence

Receive native HTML and JSON reports alongside trimmed reads.

reference

fastp-qc inputs and flags

3 inputs
NameTypeFlagDescription
sourceFOLDER--sourceFolder holding the FASTQ files (.fastq/.fq, optionally gzipped; each at most 4 GiB).
read1STRING--read1Path of the read 1 (or single-end) FASTQ inside the folder.
read2STRING--read2Optional path of the read 2 FASTQ inside the folder for paired-end mode.

Showing key inputs. fastp-qc exposes 3 inputs in total.

example

Run fastp-qc

fastp-qc · command
python3 /app/run.py --source ./source --read1 sample_R1.fastq --read2 sample_R2.fastq ./output

guidance

Choosing fastp-qc

Use fastp-qc when you need filtered read files as well as their QC reports. MultiQC combines existing reports; it does not perform this read trimming. Review filtering losses before downstream analysis.

faq

fastp-qc questions

source: Folder holding the FASTQ files (.fastq/.fq, optionally gzipped; each at most 4 GiB). read1: Path of the read 1 (or single-end) FASTQ inside the folder. read2: Optional path of the read 2 FASTQ inside the folder for paired-end mode.

Process single-end or paired-end FASTQ with fixed fastp defaults, quality and N filtering, a 15-base minimum length and two worker threads. Paired reads use overlap-based adapter detection. The output folder contains trimmed_R1.fastq.gz, optional trimmed_R2.fastq.gz, native fastp.json and fastp.html, fastp.log and a summary.json.

Supply a folder and relative read1 filename; read2 is optional. Files may use .fastq or .fq, optionally gzip-compressed, with a 4 GiB limit per input. The node exposes no trimming-parameter ports. Input yielding no valid reads fails instead of returning an empty success.

Use fastp-qc when you need filtered read files as well as their QC reports. MultiQC combines existing reports; it does not perform this read trimming. Review filtering losses before downstream analysis.

The public image repository gives immutable image and ORAS download commands, the expected source/notices bundle checksum and pinned upstream source directions. The accompanying OCI bundle retains the original build recipe, runtime sources and full installed notices. The Git recipe keeps primary notices and an exact layer/hash index; it does not duplicate the full installed notice tree or mirror every upstream source archive. Image, source and license notice downloads.

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Run fastp-qc yourself

The saved synthetic paired-read check reported 400 reads before filtering, 360 afterward and 120 adapter-trimmed reads. The verifier also checked both trimmed files and native reports. These are saved verifier values, not a complete report or biological sample. The command shows the container entrypoint with example paths.

Open fastp-qc in the libraryBuild a workflow with it

Facts on this page come from the live Trickest tool library.