The easiest way to install cutadapt is to use pip on the command line:

pip install --user --upgrade cutadapt

This will download the software from PyPI (the Python packaging index), and install the cutadapt binary into $HOME/.local/bin. If an old version of cutadapt exists on your system, the --upgrade parameter is required in order to install a newer version. You can then run the program like this:

~/.local/bin/cutadapt --help

If you want to avoid typing the full path, add the directory $HOME/.local/bin to your $PATH environment variable.

If the above does not work, keep reading.


Cutadapt requires this software to be installed:

  • One of Python 2.6, 2.7, 3.3 or 3.4. Python 2.7 is a bit faster than the other versions.
  • A C compiler.

Under Ubuntu, you may need to install the packages build-essential and python-dev.


If you have already downloaded and unpacked the .tar.gz file, then installation is done like this (replace “python” with “python3” to install the Python 3 version):

python install --user

If you get an error message:

error: command 'gcc' failed with exit status 1

Then check the entire error message. If it says something about a missing Python.h file, then you need to install the Python development packages. The appropriate package is called python-dev in Ubuntu (or python3-dev for Python 3).

System-wide installation

If you have root access, then you can install cutadapt system-wide by running:

sudo pip install cutadapt

This installs cutadapt into /usr/local/bin.

If you want to upgrade from an older version, use this command instead:

sudo pip install --upgrade cutadapt

Use without installation

Build the C extension module (you can try to skip this step – a compiled version of the module for Linux x86_64 is already included):

python build_ext -i

Then simply run the script from where it is, similar to this:

bin/cutadapt --help

If you get any errors, first try to explicitly request a specific Python version by running cutadapt like this:

python2.7 bin/cutadapt --help