.. 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)
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) accepted, not yet on pubmed
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
sh laa.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can
retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::
snakemake -s laa.rules -c config.yaml --cores 4 --stats stats.txt --wrapper-prefix git+file:///home/cokelaer/Work/github/forked/sequana-wrappers
Or use `sequanix <https://sequana.readthedocs.io/en/main/sequanix.html>`_ interface.
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
========= ====================================================================
0.10.0 full integration with latest wrapeprs and apptainers from damona
0.9.0 add singularity containers
0.8.0 **First release.**
========= ====================================================================
Raw data
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