Version Compatibility

Reference examples tested with: FastQC 0.12+, 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.

Adapter Trimming

Remove sequencing adapters from reads using Cutadapt (precise, flexible) or Trimmomatic (paired-end optimized).

"Trim adapters from reads" → Remove sequencing adapter sequences from FASTQ reads to prevent adapter contamination in downstream alignment.

• CLI: cutadapt -a ADAPTER -o out.fq in.fq or trimmomatic PE with ILLUMINACLIP
• CLI: fastp -i in.fq -o out.fq (auto-detects adapters)

Common Adapter Sequences