Because Cutadapt development happens on Linux, this is the best supported platform, but it should also run on macOS and Windows.
Installation with conda¶
Cutadapt is available as a Conda package from the Bioconda channel. Install miniconda if you don’t have Conda. Then follow the Bioconda installation instructions (in particular, make sure you have both bioconda and conda-forge in your channels list).
To then install Cutadapt into a new Conda environment, use this command:
conda create -n cutadaptenv cutadapt
cutadaptenv is the name of the Conda environment. You can
choose a different name.
Then activate the environment. This needs to be done every time you open a new shell before you can use Cutadapt:
conda activate cutadaptenv
Finally, check whether it worked:
This should show the Cutadapt version number.
Installation with pip¶
If Python is already installed on your system (it very likely is), you
can install Cutadapt using
pip on the command line:
python3 -m pip install --user --upgrade cutadapt
This will download the software from PyPI (the Python packaging
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.
On many systems, you can then run the program like this:
If this does not work or this prints an unexpected version number, then you need to use the full path to run the program:
Alternatively, you can avoid having to type the full path by adding the
$HOME/.local/bin to your
$PATH environment variable.
Installation on a Debian-based Linux distribution¶
Cutadapt is also included in Debian-based Linux distributions, such as Ubuntu. Simply use your favorite package manager to install Cutadapt. On the command-line, this should work
sudo apt install cutadapt
sudo apt install python3-cutadapt
Please be aware that distribution packages are very likely to be outdated. If you encounter unexpected behavior or need newer features, please use one of the other installation methods to get an up-to-date version before reporting bugs.
Cutadapt installation requires this software to be installed:
- Python 3.6 or newer
- Possibly a C compiler. For Linux, Cutadapt packages are provided as
so-called “wheels” (
.whlfiles) which come pre-compiled.
Under Ubuntu, you may need to install the packages
python3-dev to get a C compiler.
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 the problem is that you are missing Python development
python3-dev in Ubuntu).
System-wide installation (root required)¶
sudo can be dangerous and the above methods that don’t
require it are preferred. That said, if you have root access, you can install
Cutadapt system-wide by running:
sudo python3 -m pip install cutadapt
This installs cutadapt into
If you want to upgrade from an older version, use this command instead:
sudo python3 -m pip install --upgrade cutadapt
If the above does not work for you, then you can try to install Cutadapt into a virtual environment. This leads to fewer conflicts with system-installed packages:
sudo python3 -m venv /usr/local/cutadapt sudo /usr/local/cutadapt/bin/pip install cutadapt cd /usr/local/bin/ sudo ln -s ../cutadapt/bin/cutadapt
Installation on Windows¶
For some releases of Cutadapt, a single-file executable (
is made available on the
GitHub releases page. Try that
first, and if it does not work for you, please report the issue.
To install Cutadapt manually, keep reading.
There is no Bioconda package for Windows because Bioconda does not produce
Windows packages. To install Cutadapt, you can use
pip, but because
Cutadapt contains components that need to be compiled, you also need to install
Download a recent version (at least 3.6) of Python for Windows from <https://www.python.org/> and install it.
Download and install “Build Tools for Visual Studio 2019” from <https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019>. (There are many similarly named downloads on that page, ensure you get the right one.)
During installation, when the dialog about which components to install pops up, ensure that “C++ Build tools” is ticked. The download is quite big and can take a long time.
Open the command line (
cmd.exe) and run
py -m pip install cutadapt.
Test whether it worked by running
py -m cutadapt --version. You should see the version number of Cutadapt.
When running Cutadapt this way, you will need to remember to write
py -m cutadapt instead of just
pip3 uninstall cutadapt
and confirm with
y to remove the package. Under some circumstances, multiple
versions may be installed at the same time. Repeat the above command until you
get an error message in order to make sure that all versions are removed.
Installing the development version¶
We recommend that you install Cutadapt into a so-called virtual environment if you decide to use the development version. The virtual environment is a single directory that contains everything needed to run the software. Nothing else on your system is changed, so you can simply uninstall this particular version of Cutadapt by removing the directory with the virtual environment.
The following instructions work on Linux using Python 3. Make sure you have
installed the dependencies (
build-essential on Ubuntu)!
First, choose where you want to place the directory with the virtual
environment and what you want to call it. Let us assume you chose the path
~/cutadapt-venv. Then use these commands for the installation:
python3 -m venv ~/cutadapt-venv ~/cutadapt-venv/bin/python3 -m pip install --upgrade pip ~/cutadapt-venv/bin/pip install git+https://github.com/marcelm/cutadapt.git#egg=cutadapt
To run Cutadapt and see the version number, type
The reported version number will be something like
means that you are now running the version of Cutadapt that will become 2.2, and that it contains
5 changes (commits) since the previous release (2.1 in this case).