:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'chewbbaca' .. highlight: bash chewbbaca ========= .. conda:recipe:: chewbbaca :replaces_section_title: :noindex: A complete suite for gene\-by\-gene schema creation and strain identification. :homepage: https://github.com/B-UMMI/chewBBACA :license: GPL3 / GPL-3.0-only :recipe: /`chewbbaca `_/`meta.yaml `_ chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing \(wg\/cgMLST\) schemas\, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. .. conda:package:: chewbbaca |downloads_chewbbaca| |docker_chewbbaca| :versions: .. raw:: html
2.8.5-02.8.4-02.7.0-02.6.0-02.5.6-02.5.5-02.5.4-02.5.2-02.5.1-0 ``2.8.5-0``,  ``2.8.4-0``,  ``2.7.0-0``,  ``2.6.0-0``,  ``2.5.6-0``,  ``2.5.5-0``,  ``2.5.4-0``,  ``2.5.2-0``,  ``2.5.1-0``,  ``2.1.0-0``,  ``2.0.17.2-0``,  ``2.0.17.1-0``,  ``2.0.16-0``,  ``2.0.15-0``,  ``2.0.12-2``,  ``2.0.8-2``,  ``2.0.8-0``,  ``2.0.6-0``,  ``1.0-0`` .. raw:: html
:depends biopython: ``>=1.70`` :depends blast: ``>=2.9.0`` :depends clustalw: ``>=2.1`` :depends mafft: :depends numpy: ``>=1.14.0`` :depends pandas: ``>=0.22.0`` :depends plotly: ``>=1.12.9`` :depends prodigal: ``>=2.6.0`` :depends python: ``>=3`` :depends requests: ``>=2.2.1`` :depends scipy: ``>=0.13.3`` :depends sparqlwrapper: ``>=1.8.0`` :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`set-up-channels`), install with:: conda install chewbbaca and update with:: conda update chewbbaca or use the docker container:: docker pull quay.io/biocontainers/chewbbaca: (see `chewbbaca/tags`_ for valid values for ````) .. |downloads_chewbbaca| image:: https://img.shields.io/conda/dn/bioconda/chewbbaca.svg?style=flat :target: https://anaconda.org/bioconda/chewbbaca :alt: (downloads) .. |docker_chewbbaca| image:: https://quay.io/repository/biocontainers/chewbbaca/status :target: https://quay.io/repository/biocontainers/chewbbaca .. _`chewbbaca/tags`: https://quay.io/repository/biocontainers/chewbbaca?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/chewbbaca/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/chewbbaca/README.html