Bioconda is a distribution of bioinformatics software realized as a channel for the versatile Conda package manager. Key features of Conda are

  • a command line client for simple installation and dependency handling in the spirit of conda install mypackage,
  • very easy package creation,
  • a mechanism for creating isolated environments that allows different package versions to coexist.

These features turn Conda into the perfect package manager for bioinformatics, where analyses often involve the application of various tools with sometimes complicated and even conflicting dependencies or mixtures of different languages. Ultimately, the usage of Conda should help to perform reproducible science. Bioconda already contains over 1000 bioinformatics related packages.

Setup and usage

Step 1: Install Conda

To use bioconda, you need to install the Conda package manager which is most easily obtained via the Miniconda Python distribution. Miniconda can be installed to your home directory without admin priviledges.

Step 2: Setup Bioconda

After installing Miniconda, you can use the conda command to setup bioconda with:

conda config --add channels r
conda config --add channels bioconda
conda config --add channels conda-forge

The r channel is added to satisfy the R language dependencies of some packages as well as some non-R dependencies. Even if you don’t plan on installing R packages, the r channel is required for some Bioconda packages. Similarly, the conda-forge channel contains many dependencies that are not strictly for bioinformatics but that are required for Bioconda packages to work (see more at

Step 3: Install packages or create environments

Once the channels have been added, you can install packages, e.g.:

conda install bwa

Isolated environments (with e.g. specific software versions>`_ can be created via:

conda create -n myenviroment bwa=0.7.12

For more information, visit the Conda documentation or have a look at the command line options by executing:

conda --help

Step 4: Join the team

Because our time is limited, the policy is to add a package if we need it ourselves. However, we invite anybody who wants to use Conda for bioinformatics to join the team and contribute new packages. To get started, have a look at our recipes and the Conda documentation. If you don’t want to join us permanently, you can also fork the recipes repository and create pull requests.

Step 5: Spread the word

Consider adding a badge to your posters and presentations to promote that a tool can be easily installed from bioconda.



Bioconda has over 120 contributors, see here.

Bioconda is a derivative mark of Anaconda ®, a trademark of Continuum Analytics, Inc registered in the U.S. and other countries. Continuum Analytics, Inc. grants permission of the derivative use but is not associated with Bioconda.

The Bioconda channel is sponsored by Continuum Analytics.