From efee4a83fd203d90fc12c5ec5f4f5a26bf541a63 Mon Sep 17 00:00:00 2001
From: rfm-targa <rmamede@medicina.ulisboa.pt>
Date: Fri, 27 Oct 2023 15:29:07 +0100
Subject: [PATCH] Updated docs.

---
 CHEWBBACA/docs/user/help_support/faq.rst   | 10 ++++++++++
 CHEWBBACA/docs/user/modules/AlleleCall.rst | 11 +++++++++++
 2 files changed, 21 insertions(+)

diff --git a/CHEWBBACA/docs/user/help_support/faq.rst b/CHEWBBACA/docs/user/help_support/faq.rst
index 53e51929..07f85b1b 100644
--- a/CHEWBBACA/docs/user/help_support/faq.rst
+++ b/CHEWBBACA/docs/user/help_support/faq.rst
@@ -52,6 +52,16 @@ You can also download schemas compatible with chewBBACA from `Chewie-NS <https:/
 Chewie-NS allows chewBBACA users to download and update cg/wgMLST schemas, allowing the easy sharing of
 results, while ensuring the reproducibility and consistency of these steps.
 
+How can I identify genetic clusters based on the results generated by the AlleleCall module?
+............................................................................................
+We recommend that you use `ReporTree <https://github.com/insapathogenomics/ReporTree>`_ to identify genetic clusters
+based on the allelic profiles (contained in the ``results_alleles.tsv`` output file) determined by chewBBACA. ReporTree
+includes functionalities to identify genetic clusters at any distance threshold level(s), obtain summary reports with relevant
+statistics computed based on sample metadata, identify regions of cluster stability, etc. Cluster nomenclature can be maintained
+and updated in subsequent analyses, which is especially useful in surveillance-oriented workflows. Check the
+`publication <https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-023-01196-1>`_ and the
+`GitHub repository <https://github.com/insapathogenomics/ReporTree>`_ to know more about ReporTree.
+
 Is it possible to perform allele calling without adding novel alleles to the schema?
 ....................................................................................
 Yes, you can use the ``--no-inferred`` parameter to specify that you do not want to add novel alleles
diff --git a/CHEWBBACA/docs/user/modules/AlleleCall.rst b/CHEWBBACA/docs/user/modules/AlleleCall.rst
index 987ce20f..0bbb2740 100644
--- a/CHEWBBACA/docs/user/modules/AlleleCall.rst
+++ b/CHEWBBACA/docs/user/modules/AlleleCall.rst
@@ -412,6 +412,17 @@ Example for the ``SAMD00008628`` genome:
   algorithm to create a TSV file, ``results_alleles_hashed.tsv``, with hashed profiles (each allele identifier is substituted
   by the hash of the DNA sequence).
 
+Identify genetic clusters
+:::::::::::::::::::::::::
+
+We recommend that you use `ReporTree <https://github.com/insapathogenomics/ReporTree>`_ to identify genetic clusters
+based on the allelic profiles (contained in the ``results_alleles.tsv`` output file) determined by chewBBACA. ReporTree
+includes functionalities to identify genetic clusters at any distance threshold level(s), obtain summary reports with relevant
+statistics computed based on sample metadata, identify regions of cluster stability, etc. Cluster nomenclature can be maintained
+and updated in subsequent analyses, which is especially useful in surveillance-oriented workflows. Check the
+`publication <https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-023-01196-1>`_ and the
+`GitHub repository <https://github.com/insapathogenomics/ReporTree>`_ to know more about ReporTree.
+
 Concurrent allele calling
 :::::::::::::::::::::::::