albert-ying/autonomous-lab/trimmomatic

Trimmomatic - Read Quality Trimming

When to Use

Use Trimmomatic to trim adapter sequences and low-quality bases from Illumina sequencing reads.

Standard Workflow

1. Install: conda install -c bioconda trimmomatic
2. Run: trimmomatic PE <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> ILLUMINACLIP:<adapters.fa>:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Key Parameters

• PE: paired-end mode
• ILLUMINACLIP: adapter trimming (adapter_file:seed_mismatches:palindrome_clip_threshold:simple_clip_threshold)
• LEADING/TRAILING: remove leading/trailing low quality bases
• SLIDINGWINDOW: sliding window trimming (window_size:required_quality)
• MINLEN: minimum read length after trimming

Key Decisions

• Use TruSeq3-PE.fa for TruSeq adapters
• Adjust quality thresholds based on FastQC results