adaptertrimming

Adapter trimming is the computational process of removing adapter sequences from sequencing reads. Adapters are short strings used during library preparation to enable sequencing, but when fragments are shorter than the read length or when reads extend into the adapter, non-biological sequences can appear at the ends of reads. Removing these adapters is essential for accurate alignment, assembly, and downstream analyses such as variant calling.

Trimming can be performed in several ways. Many workflows use known adapter sequences provided by the library kit, while others detect adapters de novo by identifying overrepresented sequences in the data. Common tools for adapter trimming include Cutadapt, Trimmomatic, AdapterRemoval, BBduk, and fastp. Functions often include trimming of 5' and/or 3' ends, matching partial adapters, quality-based trimming, and length filtering to discard reads that fall below a minimum length after trimming.

Typical workflow steps involve specifying the adapter sequences (or enabling automatic detection), choosing whether to trim adapters from one or both ends, setting quality thresholds, and defining a minimum read length post-trimming. Output usually includes trimmed reads, optional unpaired reads, and a summary report of how many reads and bases were removed. Reads that become too short after trimming are commonly discarded.

Quality control is recommended after trimming, for example with FastQC or similar tools, to verify the absence of residual adapter content and to assess read quality. Proper adapter trimming improves the reliability of downstream analyses and reduces artifacts caused by adapter contamination.