Cutadapt

Cutadapt finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences from high-throughput sequencing reads. Additionally, it can modify, filter, and demultiplex reads in various ways. Its output consists of all sequences edited, including those reduced to zero. For input, you provide the adapter sequence to be trimmed and an input FASTQ file.

For additional information, see the Cutadapt documentation.

ml biocontainers cutadapt
cutadapt -a <Adapter Seq> -o output.fastq input.fastq

Parallel Capabilities: Single core default, multithreading options supported.