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Cutadapt version 1.8.3

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General Description

Cutadapt version 1.83

Basic Usage


Useful Options

cutadapt version 1.8.3
Copyright (C) 2010-2015 Marcel Martin <>

cutadapt removes adapter sequences from high-throughput sequencing reads.

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

For paired-end reads:
    cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq

Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
characters are supported. 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, .xz, .bz2). Use the file name '-' for
standard input/output. Without the -o option, output is sent to standard output.

Some other available features are:
  * Various other adapter types (5' adapters, "mixed" 5'/3' adapters etc.)
  * Trimming a fixed number of bases
  * Quality trimming
  * Trimming colorspace reads
  * Filtering reads by various criteria

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

Further Information

See the official website: [http:// ]