Version Compatibility

Reference examples tested with: Trimmomatic 0.39+, cutadapt 4.4+, fastp 0.23+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Quality Filtering

Trim low-quality bases and filter reads using Trimmomatic sliding window or fastp quality filtering.

"Filter reads by quality" → Remove low-quality bases and discard reads below quality/length thresholds.

• CLI: trimmomatic PE with SLIDINGWINDOW and MINLEN options
• CLI: fastp --qualified_quality_phred 20 --length_required 50

Trimmomatic Quality Operations

Single-End Mode

trimmomatic SE -phred33 \
    input.fastq.gz output.fastq.gz \
    LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Paired-End Mode

trimmomatic PE -phred33 -threads 4 \
    input_R1.fastq.gz input_R2.fastq.gz \
    output_R1_paired.fastq.gz output_R1_unpaired.fastq.gz \
    output_R2_paired.fastq.gz output_R2_unpaired.fastq.gz \
    LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Trimmomatic Operations

Operation	Syntax	Description
LEADING	LEADING:Q	Remove leading bases below quality Q
TRAILING	TRAILING:Q	Remove trailing bases below quality Q
SLIDINGWINDOW	SLIDINGWINDOW:W:Q	Cut when W-bp window average < Q