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<!DOCTYPE html>
<html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<title>GPS :: Global Pneumococcal Sequencing Project</title>
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<h1><i class="fa fa-pencil-square-o blue"></i> Training: Command Line</h1>
</header>
<div class="desc">
<!-- TODO: add training command line -->
<h2>In silico serotyping</h2>
<p>Install SeroBA (<a target="_blank"
href="https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000186">Epping et al
2018</a>) as per instructions at <a target="_blank"
href="https://github.com/sanger-pathogens/seroba#installation">https://github.com/sanger-pathogens/seroba#installation</a>
and git clone the database from the following link <a target="_blank"
href="https://github.com/sanger-pathogens/seroba.git">https://github.com/sanger-pathogens/seroba.git</a>.
</p>
<p>Files required to run serotyping using SeroBA:</p>
<ol>
<li>paired-end fastq files</li>
<li>database</li>
<li>sample list (only for running on multiple samples)</li>
</ol>
<p>Run in silico serotyping on a single sample:
<pre>serotype runSerotyping <full path to the database> <read 1> <read 2> <output folder prefix></pre>
</p>
<p>Run in silico serotyping on multiple samples:</p>
<ol>
<li>
create a list of sample names and save it as samplelist (e.g. the sample name for
<em>24371_8#283_1.fastq.gz</em> is <em>24371_8#283</em>)
</li>
<li>
<pre>for f in $(cat samplelist); do seroba runSerotyping <path to the database> ${f}_1.fastq.gz ${f}_2.fastq.gz ${f}; done</pre>
</li>
<li>
<pre>seroba summary ./</pre>
</li>
</ol>
<p>
<strong>Output:</strong>
<br>
summary.tsv
</p>
<p>
These instructions are available to download here:
<br />
<a download class="btn btn-info white"
title="In Silico serotyping instructions" target="_blank"
aria-label="Download the In Silico serotyping instructions"
href="in-silico-serotyping.txt">
<i class="fa fa-download white fa-lg"></i>
Download
</a>
</p>
<p></p>
<h2>GPSC assignment</h2>
<p>
Install PopPUNK 2.4 as per instructions at <a target="_blank" title="PopPUNK2 installation instructions"
aria-label="Open the PopPUNK2 installation instructions in a new window"
href="https://poppunk.readthedocs.io/en/latest/installation.html">PopPUNK documentation</a>
and download the GPS reference database and the GPS designation.
</p>
<p>
GPS reference database (n=42,163):
<br />
<a download class="btn btn-info white"
title="GPS reference database" target="_blank"
aria-label="Download the GPS reference database"
href="https://gps-project.cog.sanger.ac.uk/GPS_v6.zip">
<i class="fa fa-download white fa-lg"></i>
Download
</a>
</p>
<p>
GPS designation (933 GPSCs):
<br />
<a download class="btn btn-info white"
title="GPS designation CSV file" target="_blank"
aria-label="Download the GPS designation CSV file"
href="GPS_v6_external_clusters.csv">
<i class="fa fa-download white fa-lg"></i>
Download
</a>
</p>
<p>Files required to run GPSC assignment using PopPUNK 2.4:</p>
<ol>
<li>
A 2-column tab-delimited file containing sample name and path to the corresponding assembly (no header)
</li>
<li>
GPS reference database <GPS_v6>
</li>
<li>
GPS designation <GPS_v6_external_clusters.csv>
</li>
</ol>
<p>
output directory name is assigned using <em>--output</em>
<br>
number of threads can be changed using <em>–threads</em>
</p>
<p>Run GPSC assignment:</p>
<pre>poppunk_assign --db GPS_v6 --distances GPS_v6/GPS_v6.dists --query <2-column path to assembly> --output <GPSC_assignment> --external-clustering GPS_v6_external_clusters.csv</pre>
<p>
<strong>Outputs:</strong>
<br>
<em>_clusters.csv</em>: popPUNK clusters with dataset specific nomenclature
<br>
<em>_external_clusters.csv</em>: GPSC v6 scheme designations
</p>
<p>
<strong>Novel Clusters are assigned NA</strong> in the <em>_external_clusters.csv</em> as they have not been defined in the v6 dataset used to designate the GPSCs. Please email: <a href="mailto:globalpneumoseq@gmail.com">globalpneumoseq@gmail.com</a> to have novel clusters added to the database and a GPSC cluster name assigned after you have checked for low level contamination which may contribute to biased accessory distances.
</p>
<p>
Merged clusters: Unsampled diversity may represent missing variation linking two clusters. GPSCs are then merged. For example if GPSC23 and GPSC362 merged, the GPSC would be then reported as GPSC23, with a merge history of GPSC23;362.
</p>
<p>
The instructions for PopPUNK v2.4 are available to download
<br />
<a download class="btn btn-info white"
title="Instructions for PopPUNK v2.4" target="_blank"
aria-label="Download the instructions for PopPUNK v2.4"
href="GPSC_README_PopPUNK2.txt">
<i class="fa fa-download white fa-lg"></i>
Download
</a>
</p>
<p>
The instructions for PopPUNK v1 are available to download
<br />
<a download class="btn btn-info white"
title="Instructions for PopPUNK v1" target="_blank"
aria-label="Download the instructions for PopPUNK v1"
href="GPSC_README_PopPUNK1.txt">
<i class="fa fa-download white fa-lg"></i>
Download
</a>
</p>
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