.. ############################
.. _saureus-report:
.. ############################

Staphylococcus aureus report
############################

.. only:: html

    :Version: |version|
    :Date: |today|
    
.. toctree::
   :hidden:
   
   sccmec.rst
   spatyping.rst

.. contents::

We followed the standard European external Quality Control (EQC) project 
:cite:`Deplano2018` to standarize the reported results when *S. aureus* samples
are analyzed.

Genes to report
===============

A list of important genes is provided in file: 

.. csv-table::
   :widths: 4,12,25
   :header-rows: 1 
   :file: EQC_genes-description.csv
   
   
.. test: :file: ../../../../BacterialTyper/report/Staphylococcus/EQC_genes.csv
    
.. include:: sccmec.rst

.. include:: spatyping.rst

.. ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/006/ERR2112496/ERR2112496_1.fastq.gz
.. ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/006/ERR2112496/ERR2112496_2.fastq.gz