:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'pgcgap'
.. highlight: bash

pgcgap
======

.. conda:recipe:: pgcgap
   :replaces_section_title:
   :noindex:

   A prokaryotic genomics and comparative genomics analysis pipeline

   :homepage: https://github.com/liaochenlanruo/pgcgap/blob/master/README.md
   :documentation: https://liaochenlanruo.fun/pgcgap/
   
   :developer docs: https://github.com/liaochenlanruo/pgcgap/tree/master
   :license: GPL / GPLv3
   :recipe: /`pgcgap <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pgcgap>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pgcgap/meta.yaml>`_
   :links: biotools: :biotools:`pgcgap`

   PGCGAP is a pipeline for prokaryotic comparative genomics analysis. It can take the pair\-end reads\, ONT reads or PacBio reads as input. In addition to genome assembly\, gene prediction and annotation\, it can also get common comparative genomics analysis results such as phylogenetic trees of single\-core proteins and core SNPs\, pan\-genome\, whole\-genome Average Nucleotide Identity \(ANI\)\, orthogroups and orthologs\, COG annotations\, substitutions \(SNPs\) and insertions\/deletions \(indels\)\, and antimicrobial and virulence genes mining with only one line of commands.


.. conda:package:: pgcgap

   |downloads_pgcgap| |docker_pgcgap|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.0.35-0</code>,  <code>1.0.34-0</code>,  <code>1.0.33-0</code>,  <code>1.0.32-0</code>,  <code>1.0.31-0</code>,  <code>1.0.30-0</code>,  <code>1.0.29-0</code>,  <code>1.0.28-0</code>,  <code>1.0.27-0</code>,  </span></summary>
      

      ``1.0.35-0``,  ``1.0.34-0``,  ``1.0.33-0``,  ``1.0.32-0``,  ``1.0.31-0``,  ``1.0.30-0``,  ``1.0.29-0``,  ``1.0.28-0``,  ``1.0.27-0``,  ``1.0.26-0``,  ``1.0.25-0``,  ``1.0.24-0``,  ``1.0.23-0``,  ``1.0.22-0``,  ``1.0.21-0``,  ``1.0.20-0``,  ``1.0.19-2``,  ``1.0.19-1``,  ``1.0.19-0``,  ``1.0.18-1``,  ``1.0.18-0``,  ``1.0.17-0``,  ``1.0.16-0``,  ``1.0.15-0``,  ``1.0.14-0``,  ``1.0.13-1``,  ``1.0.13-0``,  ``1.0.12-1``,  ``1.0.12-0``,  ``1.0.11-1``,  ``1.0.11-0``,  ``1.0.10-2``,  ``1.0.10-1``,  ``1.0.10-0``,  ``1.0.9-2``,  ``1.0.9-1``,  ``1.0.9-0``,  ``1.0.8-0``,  ``1.0.7-0``,  ``1.0.6-0``,  ``1.0.5-0``,  ``1.0.4-0``,  ``1.0.3-0``,  ``1.0.2-4``,  ``1.0.2-3``,  ``1.0.2-2``,  ``1.0.2-1``,  ``1.0.1-1``,  ``1.0.1-0``,  ``1.0.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends abricate: ``1.0.1.*``
   :depends abyss: ``2.3.4.*``
   :depends canu: ``2.1.1.*``
   :depends coreutils: ``9.0.*``
   :depends fastani: ``1.33.*``
   :depends fastp: ``0.23.2.*``
   :depends htslib: ``1.15.1.*``
   :depends mamba: ``0.22.1.*``
   :depends mash: ``2.3.*``
   :depends matplotlib-base: ``3.5.1.*``
   :depends muscle: ``5.1.*``
   :depends numpy: ``1.21.5.*``
   :depends openjdk: 
   :depends orthofinder: ``2.5.4.*``
   :depends pal2nal: ``14.1.*``
   :depends panaroo: ``1.2.10.*``
   :depends pandas: ``1.3.5.*``
   :depends perl: ``>=5.32.1,<6.0a0 *_perl5``
   :depends perl-data-dumper: 
   :depends perl-file-copy-recursive: 
   :depends perl-file-tee: 
   :depends perl-parallel-forkmanager: 
   :depends perl-pod-usage: 
   :depends perl-posix: 
   :depends prokka: ``>=1.14.5``
   :depends r-base: ``>=4.1.1``
   :depends r-corrplot: 
   :depends r-ggplot2: 
   :depends r-gplots: 
   :depends r-pheatmap: 
   :depends r-plotrix: 
   :depends seaborn: ``0.11.2.*``
   :depends sickle-trim: ``1.33.*``
   :depends snippy: ``4.6.0.*``
   :depends snpeff: ``5.0.*``
   :depends trimal: ``1.4.1.*``
   :depends unicycler: ``0.5.0.*``
   :depends wget: ``1.20.3.*``
   :requirements:

   .. rubric:: Installation

   With an activated Bioconda channel (see :ref:`set-up-channels`), install with::

      conda install pgcgap

   and update with::

      conda update pgcgap

   or use the docker container::

      docker pull quay.io/biocontainers/pgcgap:<tag>

   (see `pgcgap/tags`_ for valid values for ``<tag>``)


.. |downloads_pgcgap| image:: https://img.shields.io/conda/dn/bioconda/pgcgap.svg?style=flat
   :target: https://anaconda.org/bioconda/pgcgap
   :alt:   (downloads)
.. |docker_pgcgap| image:: https://quay.io/repository/biocontainers/pgcgap/status
   :target: https://quay.io/repository/biocontainers/pgcgap
.. _`pgcgap/tags`: https://quay.io/repository/biocontainers/pgcgap?tab=tags


.. raw:: html

    <script>
        var package = "pgcgap";
        var versions = ["1.0.35","1.0.34","1.0.33","1.0.32","1.0.31"];
    </script>






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-----------------

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    :file: ../../templates/package_dashboard.html

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