General Description

Basic Usage

module load bio #to load all bio modules
module load cio/cutadapt/1.6 #to load cutadapt alone

Useful Options

cutadapt version 1.6
Copyright (C) 2010-2014 Marcel Martin <>

cutadapt removes adapter sequences from high-throughput sequencing reads.

    cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq

Replace "ADAPTER" with the actual sequence of your 3' adapter. The sequence may
contain 'N' wildcard characters. The reverse complement is *not* automatically
searched. All reads from input.fastq will be written to output.fastq with the
adapter sequence removed. Adapter matching is error-tolerant. Multiple adapter
sequences can be given (use further -a options), but only the best-matching
adapter will be removed.

Input may also be in FASTA format. Compressed input and output is supported and
auto-detected from the file name (.gz or .bz2). Use the file name '-' for
standard input/output. Without the -o option, output is sent to standard output.

Some other available features are:
  * Trimming of 5' adapters and "mixed" 5'/3' adapters
  * Trimming a fixed number of bases
  * Quality trimming
  * Trimming paired-end reads
  * Trimming colorspace reads
  * Filtering reads by various criteria

See for the full documentation.
Use "cutadapt --help" to see all command-line options.

Further Information

See the official website: [http:// ]