Kleborate

data_analysis/kleborate.rst

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+.. index::
+   single: Kleborate
+
+.. _kleborate:
+
+*********
+Kleborate
+*********
+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