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+Hi, I’m GECCO!
+==============
+
+🦎 ️Overview
+---------------
+
+GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast
+and scalable method for identifying putative novel Biosynthetic Gene
+Clusters (BGCs) in genomic and metagenomic data using Conditional Random
+Fields (CRFs).
+
+|GitLabCI| |License| |Coverage| |Docs| |Source| |Mirror| |Changelog|
+|Issues| |Preprint| |PyPI| |Bioconda| |Versions| |Wheel|
+
+🔧 Installing GECCO
+-------------------
+
+GECCO is implemented in `Python <https://www.python.org/>`__, and
+supports `all versions <https://endoflife.date/python>`__ from Python
+3.6. It requires additional libraries that can be installed directly
+from `PyPI <https://pypi.org>`__, the Python Package Index.
+
+Use ```pip`` <https://pip.pypa.io/en/stable/>`__ to install GECCO on
+your machine:
+
+.. code:: console
+
+   $ pip install gecco-tool
+
+If you’d rather use `Conda <https://conda.io>`__, a package is available
+in the ```bioconda`` <https://bioconda.github.io/>`__ channel. You can
+install with:
+
+.. code:: console
+
+   $ conda install -c bioconda gecco
+
+This will install GECCO, its dependencies, and the data needed to run
+predictions. This requires around 100MB of data to be downloaded, so it
+could take some time depending on your Internet connection. Once done,
+you will have a ``gecco`` command available in your $PATH.
+
+*Note that GECCO uses*\ `HMMER3 <http://hmmer.org/>`__\ *, which can
+only run on PowerPC and recent x86-64 machines running a POSIX operating
+system. Therefore, Linux and OSX are supported platforms, but GECCO will
+not be able to run on Windows.*
+
+🧬 Running GECCO
+-----------------
+
+Once ``gecco`` is installed, you can run it from the terminal by giving
+it a FASTA or GenBank file with the genomic sequence you want to
+analyze, as well as an output directory:
+
+.. code:: console
+
+   $ gecco run --genome some_genome.fna -o some_output_dir
+
+Additional parameters of interest are:
+
+-  ``--jobs``, which controls the number of threads that will be spawned
+   by GECCO whenever a step can be parallelized. The default, *0*, will
+   autodetect the number of CPUs on the machine using
+   ```os.cpu_count`` <https://docs.python.org/3/library/os.html#os.cpu_count>`__.
+-  ``--cds``, controlling the minimum number of consecutive genes a BGC
+   region must have to be detected by GECCO (default is 3).
+-  ``--threshold``, controlling the minimum probability for a gene to be
+   considered part of a BGC region. Using a lower number will increase
+   the number (and possibly length) of predictions, but reduce accuracy.
+
+🔖 Reference
+-------------
+
+GECCO can be cited using the following preprint:
+
+   **Accurate de novo identification of biosynthetic gene clusters with
+   GECCO**. Laura M Carroll, Martin Larralde, Jonas Simon Fleck, Ruby
+   Ponnudurai, Alessio Milanese, Elisa Cappio Barazzone, Georg Zeller.
+   bioRxiv 2021.05.03.442509;
+   `doi:10.1101/2021.05.03.442509 <https://doi.org/10.1101/2021.05.03.442509>`__
+
+💭 Feedback
+------------
+
+⚠️ Issue Tracker
+~~~~~~~~~~~~~~~~
+
+Found a bug ? Have an enhancement request ? Head over to the `GitHub
+issue tracker <https://github.com/zellerlab/GECCO/issues>`__ if you need
+to report or ask something. If you are filing in on a bug, please
+include as much information as you can about the issue, and try to
+recreate the same bug in a simple, easily reproducible situation.
+
+🏗️ Contributing
+~~~~~~~~~~~~~~~~
+
+Contributions are more than welcome! See
+```CONTRIBUTING.md`` <https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md>`__
+for more details.
+
+⚖️ License
+----------
+
+This software is provided under the `GNU General Public License v3.0 or
+later <https://choosealicense.com/licenses/gpl-3.0/>`__. GECCO is
+developped by the `Zeller
+Team <https://www.embl.de/research/units/scb/zeller/index.html>`__ at
+the `European Molecular Biology Laboratory <https://www.embl.de/>`__ in
+Heidelberg.
+
+.. |GitLabCI| image:: https://img.shields.io/gitlab/pipeline/grp-zeller/GECCO/master?gitlab_url=https%3A%2F%2Fgit.embl.de&style=flat-square&maxAge=600
+   :target: https://git.embl.de/grp-zeller/GECCO/-/pipelines/
+.. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg?style=flat-square&maxAge=2678400
+   :target: https://choosealicense.com/licenses/gpl-3.0/
+.. |Coverage| image:: https://img.shields.io/codecov/c/gh/zellerlab/GECCO?style=flat-square&maxAge=600
+   :target: https://codecov.io/gh/zellerlab/GECCO/
+.. |Docs| image:: https://img.shields.io/badge/docs-gecco.embl.de-green.svg?maxAge=2678400&style=flat-square
+   :target: https://gecco.embl.de
+.. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square
+   :target: https://github.com/zellerlab/GECCO/
+.. |Mirror| image:: https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square&maxAge=2678400
+   :target: https://git.embl.de/grp-zeller/GECCO/
+.. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square
+   :target: https://github.com/zellerlab/GECCO/blob/master/CHANGELOG.md
+.. |Issues| image:: https://img.shields.io/github/issues/zellerlab/GECCO.svg?style=flat-square&maxAge=600
+   :target: https://github.com/zellerlab/GECCO/issues
+.. |Preprint| image:: https://img.shields.io/badge/preprint-bioRxiv-darkblue?style=flat-square&maxAge=2678400
+   :target: https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1
+.. |PyPI| image:: https://img.shields.io/pypi/v/gecco-tool.svg?style=flat-square&maxAge=3600
+   :target: https://pypi.python.org/pypi/gecco-tool
+.. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/gecco?style=flat-square&maxAge=3600
+   :target: https://anaconda.org/bioconda/gecco
+.. |Versions| image:: https://img.shields.io/pypi/pyversions/gecco-tool.svg?style=flat-square&maxAge=3600
+   :target: https://pypi.org/project/gecco-tool/#files
+.. |Wheel| image:: https://img.shields.io/pypi/wheel/gecco-tool?style=flat-square&maxAge=3600
+   :target: https://pypi.org/project/gecco-tool/#files