mini-prep

This Nextflow workflow processes paired-end sequencing reads by:

1. Quality trimming and filtering with fastp
2. Removing contaminant sequences using bbmap
3. Taxonomically classifying the clean reads using kraken2
4. Report using multiqc

Prerequisites

• BBMap database: Must contain /ref/index/ directory
• Kraken2 database: Must contain hash.k2d file

Usage

nextflow run main.nf --input_pattern "path/to/reads/*_{1,2}.fastq.gz" \
                     --contaminants_db "path/to/bbmap_db" \
                     --kraken_db "path/to/kraken_db"

Workflow Steps

graph TD
    A[Input Reads] --> B[FASTP]
    B --> C[BBMAP]
    C --> D[Clean Reads]
    C --> E[Mapped Contaminants]
    E --> F[SAMTOOLS_STATS]
    D --> G[KRAKEN]
    B --> H[QC Reports]
    F --> H
    H --> I[MULTIQC]

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Outputs

• Quality-filtered and contaminant-free reads
• Taxonomic classification of clean reads
• Comprehensive QC reports (FASTP, SAMTOOLS_STATS, MULTIQC)

Note

Materials prepared for a training session at the Quadram Institute.