.. index::
   single: Kleborate

.. _kleborate:

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Kleborate
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Kleborate is a tool that can be used to screen assemblies of *Klebsiella* 
*pneumoniae* and the *Klebsiella pneumoniae* species complex (KpSC) for:

 * MLST sequence type
 * species (e.g. *K. pneumoniae*, *K. quasipneumoniae*, *K. variicola*, etc.)
 * ICE *Kp* associated virulence loci: yersiniabactin (*ybt*), colibactin (*clb*),
   salmochelin (*iro*), hypermucoidy (*rmpA*)
 * virulence plasmid associated loci: salmochelin (*iro*), aerobactin (*iuc*), 
   hypermucoidy (*rmpA*, *rmpA2*)
 * antimicrobial resistance determinants: acquired genes, SNPs, gene truncations
   and intrinsic β-lactamases
 * K (capsule) and O antigen (LPS) serotype prediction, via *wzi* alleles and
   Kaptive.
   
Kleborate and Kaptive are described in 
Lam *et al.* 2021 *Nat Commun* **12:** 4188 
(`PubMed: 34234121 <https://pubmed.ncbi.nlm.nih.gov/34234121/>`_) and 
Lam *et al.* 2022 *Microb Genom* **8:** 000800 
(`PubMed: 35311639 <https://pubmed.ncbi.nlm.nih.gov/35311639/>`_) respectively.

Kleborate will usually only be available on databases hosting suitable data
i.e. *Klebsiella* isolates.

The function can be accessed by selecting the 'Analysis' section on the main 
contents page.

.. image:: /images/data_analysis/kleborate.png

Jump to the ‘Third party’ category, follow the link to Kleborate, then click 
‘Launch Kleborate’.

.. image:: /images/data_analysis/kleborate2.png

Alternatively, it can be accessed following a query by clicking the ‘Kleborate’ 
button in the 'Third party' list at the bottom of the results table. Please 
note that the list of functions here may vary depending on the setup of the 
database.

.. image:: /images/data_analysis/kleborate3.png

Select the isolate records to analyse - these will be pre-selected if you 
accessed the plugin following a query. You can then choose the analysis to run:

* Basic screening for species, MLST and virulence loci
* As above and turn on screening for resistance genes (--resistance)
* As above and turn on screening for K & O antigen loci (--all)

Click submit.

.. image:: /images/data_analysis/kleborate4.png

The analysis will be submitted to the job queue.

When the job has completed you will see a table of results that is also 
available for download in tab-delimited text and Excel formats.

.. image:: /images/data_analysis/kleborate5.png