civet.html

---
layout: default
---

<div class="content">
  <header>
    <h1>civet</h1>
  </header>
  <div class="contrib">
    <h5>Cluster Investigation and Virus Epidemiology Tool</h5>

    <p>civet was developed to aid SARS-CoV-2 outbreak investigations and enable robust analysis to be performed and reports generated as rapidly as the data was being produced. </p>
  
  <p>civet puts new sequences into the context of known background diversity, and can summarise the background diversity based on the users input.</p>
  <h5>How to cite</h5>
  <p>O'Toole et al 2021. medRxiv preprint https://doi.org/10.1101/2021.12.13.21267267 </p>
</div>
</div>
<div id="pangolin_grid">
    <div>
      <br>
      <br>
      <h3>Civet Documentation</h3>
    </div>
    <div>
      <a href="https://github.com/cov-ert/civet3" class="image"><img src="../assets/images/civet.png" style="max-height:300px;max-width:320px" alt="" /></a>
  </div>
  </div>

<h2>Quick start walkthrough</h2>
<div id="pangolin_link_grid">
  <div class="contrib"><a href="{{ 'resources/civet/walkthrough.html' | absolute_url }}">Quick start</a></div>
  <div class="contrib"><a href="https://github.com/artic-network/civet/tree/master/quickstart_data">Quick start data</a></div>
</div>

<h2>Example reports</h2>
<div id="pangolin_link_grid">
  <div class="contrib"><a href="{{ 'resources/civet/report.html' | absolute_url }}">Example civet report</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/civet_case_study_1.html' | absolute_url }}">Example Case study 1</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/civet_case_study_2.html' | absolute_url }}">Example Case study 2</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/civet_case_study_3.html' | absolute_url }}">Example Case study 3</a></div>
</div>

<h2>Installation and updating</h2>
<div id="pangolin_link_grid">
  <div class="contrib"><a href="{{ 'resources/civet/requirements.html' | absolute_url }}">Dependencies</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/walkthrough.html#installation' | absolute_url }}">Installation</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/walkthrough.html#check_the_install_worked' | absolute_url }}">Check the install worked</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/walkthrough.html#updating' | absolute_url }}">Updating</a></div>
</div>

<h2>Background data set & setting up your first civet run</h2>
<div id="pangolin_link_grid">
  <div class="contrib"><a href="{{ 'resources/civet/setup_for_CLIMB.html' | absolute_url }}">Setup for CLIMB users</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/walkthrough.html#background_dataset' | absolute_url }}">Walkthrough of getting an example background dataset</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/background_data.html' | absolute_url }}">Background dataset</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/background_column_configuration.html' | absolute_url }}">Background column configuration</a></div>
</div>


<h2>Running civet</h2>
<div id="pangolin_link_grid">
  <div class="contrib"><a href="{{ 'resources/civet/walkthrough.html#example_use_cases' | absolute_url }}">Example use cases walkthrough</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/pipeline_description.html' | absolute_url }}">Full Pipeline Description</a></div>
</div>

<h2>Run options and configuration</h2>
<div id="pangolin_link_grid">
  <div class="contrib"><a href="{{ 'resources/civet/input_options.html' | absolute_url }}">Input options</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/input_sequences_options.html' | absolute_url }}">Input sequences options</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/input_column_configuration.html' | absolute_url }}">Input column configuration</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/output_options.html' | absolute_url }}">Output options</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/catchment_options.html' | absolute_url }}">Catchment options</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/report_configuration_options.html' | absolute_url }}">Report configuration options</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/table_options.html' | absolute_url }}">Table options</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/timeline_options.html' | absolute_url }}">Timeline options</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/map_options.html' | absolute_url }}">Map options</a></div>
  <div class="contrib"><a href="{{ 'resources/civet/tree_options.html' | absolute_url }}">Tree visualisation options</a></div>
</div>

<h2>References</h2>
<div id="pangolin_link_grid">
<div class="contrib"><a href="{{ 'resources/civet/references.html' | absolute_url }}">References</a></div>
</div>