fastp

A tool designed to provide ultrafast all-in-one preprocessing and quality control for FastQ data.
fastp supports batch processing of multiple FASTQ files in a folder, see - batch processing
If you use fastp in your work, you can cite fastp as: Shifu Chen. fastp 1.0: An ultra-fast all-round tool for FASTQ data quality control and preprocessing. iMeta 4.5 (2025): e70078 https://doi.org/10.1002/imt2.70078

Workflow

1. Input paired-end reads
   Upload paired-end FASTQ files, including R1 and R2 reads.

2. Quality filtering and deduplication
   Run fastp with adapter/quality filtering and duplication removal enabled. Reads with too many low-quality bases are removed, and reads shorter than the required length are discarded.

3. Generate clean reads
   Output filtered clean paired-end reads: _clean_R1.fastq.gz and _clean_R2.fastq.gz.

4. Summarize QC results
   Generate a QC summary table reporting total reads, clean reads, and clean bases for quick review before downstream analysis.

Data

Example dataset include 100 bp illumina WGS reads consist of ~10% subsets of 3 paired end sets of reads from the following publication:
The sample names in the original publication used to generate the toy dataset is ERR260162 (sample1)

Result：

v2.0:The pipeline is stored in Code Repository: CRS1225977902999547904. The computational docker enrionment is stored in Software Repository: SRS1225987480378159104.

Reproducibility

The pipeline utilizes code CRS1225977902999547904 and Docker image SRS1225987480378159104, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'Fastp'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.