Metadata-Version: 2.4
Name: sequana-laa
Version: 0.12.0
Summary: Long read amplicon analysis
License: BSD-3
License-File: LICENSE
Keywords: snakemake,NGS,sequana,amplicon,long reads
Author: Sequana Team
Requires-Python: >=3.8,<4.0
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: License :: Other/Proprietary License
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Dist: click (>=8.1.7,<9.0.0)
Requires-Dist: pulp (>=2.8)
Requires-Dist: rich-click (>=1.7.2,<2.0.0)
Requires-Dist: sequana (>=0.18.0)
Requires-Dist: sequana-pipetools (>=0.16.6)
Requires-Dist: sequana-wrappers (>=26.4.1)
Requires-Dist: snakemake (>=7.32)
Project-URL: Repository, https://github.com/sequana/laa
Description-Content-Type: text/x-rst


.. image:: https://badge.fury.io/py/sequana-laa.svg
     :target: https://pypi.python.org/pypi/sequana_laa

.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
    :target: http://joss.theoj.org/papers/10.21105/joss.00352
    :alt: JOSS (journal of open source software) DOI

.. image:: https://github.com/sequana/laa/actions/workflows/main.yml/badge.svg
   :target: https://github.com/sequana/laa/actions/workflows/main.yml)

.. image:: https://img.shields.io/badge/python-3.11%20%7C%203.12-blue.svg
    :target: https://pypi.python.org/pypi/sequana_laa
    :alt: Python 3.11 | 3.12



This is is the **laa** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project

:Overview: Perform amplicon analysis on Pacbio data sets including variant and phylogeny
:Input: A set of CCS files from pacbio in FastQ formats
:Output: variant calling, phylogney, consensus genomes, etc
:Status: production but may change
:Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352

This pipeline was used in :

- L'Honneur et al (polyomavirus, 2022) https://pubmed.ncbi.nlm.nih.gov/34979561/ 
- Kali et al (rabies,2021), https://pubmed.ncbi.nlm.nih.gov/33444703/
- Claireaux et al. (gene involved in HIV, 2022) https://pubmed.ncbi.nlm.nih.gov/35082297/

Installation
~~~~~~~~~~~~

You must install Sequana first::

    pip install sequana

Then, just install this package::

    pip install sequana_laa


Usage
~~~~~

::

    sequana_laa --help
    sequana_laa --input-directory DATAPATH 

This creates a directory with the pipeline and configuration file. You will then need 
to execute the pipeline::

    cd laa
    bash laa.sh  # for a local run

This launches a snakemake pipeline.

Requirements
~~~~~~~~~~~~

This pipelines requires the following executable(s):

- vt
- freebayes
- igvtools
- sequana
- snpeff (optional)
- samtools
- bamtools
- minimap2

.. image:: https://raw.githubusercontent.com/sequana/laa/main/sequana_pipelines/laa/dag.png


Details
~~~~~~~~~

This pipeline runs amplicon analysis on long reads data from pacbio sequencers. 


Rules and configuration details
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/laa/main/sequana_pipelines/laa/config.yaml>`_
to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. 

Changelog
~~~~~~~~~

========= ====================================================================
Version   Description
========= ====================================================================
0.12.0    * migrated to modern sequana layout (poetry, rich_click, no
            click_completion); wrapper: directives replaced by
            manager.get_shell shells or inline shell/run blocks;
            dedicated igvtools apptainer; samtools faidx rule to build
            the reference index
0.11.0    add apptainer containers
0.10.0    full integration with latest wrapeprs and apptainers from damona
0.9.0     add singularity containers
0.8.0     **First release.**
========= ====================================================================



