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README.html
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<!DOCTYPE html><html><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1"><style>@font-face {
font-family: octicons-anchor;
src: url(https://cdnjs.cloudflare.com/ajax/libs/octicons/4.4.0/font/octicons.woff) format('woff');
}
* {
box-sizing: border-box;
}
body {
width: 980px;
margin-right: auto;
margin-left: auto;
color:#333;
background:#fff;
}
body .markdown-body {
padding: 45px;
border: 1px solid #ddd;
border-radius: 3px;
word-wrap: break-word;
}
pre {
font: 12px Consolas, "Liberation Mono", Menlo, Courier, monospace;
}
.markdown-body {
-webkit-text-size-adjust: 100%;
text-size-adjust: 100%;
color: #333;
font-family: "Helvetica Neue", Helvetica, "Segoe UI", Arial, freesans, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
font-size: 16px;
line-height: 1.6;
word-wrap: break-word;
}
.markdown-body a {
background-color: transparent;
}
.markdown-body a:active,
.markdown-body a:hover {
outline: 0;
}
.markdown-body strong {
font-weight: bold;
}
.markdown-body h1 {
font-size: 2em;
margin: 0.67em 0;
}
.markdown-body img {
border: 0;
}
.markdown-body hr {
box-sizing: content-box;
height: 0;
}
.markdown-body pre {
overflow: auto;
}
.markdown-body code,
.markdown-body kbd,
.markdown-body pre {
font-family: monospace, monospace;
font-size: 1em;
}
.markdown-body input {
color: inherit;
font: inherit;
margin: 0;
}
.markdown-body html input[disabled] {
cursor: default;
}
.markdown-body input {
line-height: normal;
}
.markdown-body input[type="checkbox"] {
box-sizing: border-box;
padding: 0;
}
.markdown-body table {
border-collapse: collapse;
border-spacing: 0;
}
.markdown-body td,
.markdown-body th {
padding: 0;
}
.markdown-body input {
font: 13px / 1.4 Helvetica, arial, nimbussansl, liberationsans, freesans, clean, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
}
.markdown-body a {
color: #4078c0;
text-decoration: none;
}
.markdown-body a:hover,
.markdown-body a:active {
text-decoration: underline;
}
.markdown-body hr {
height: 0;
margin: 15px 0;
overflow: hidden;
background: transparent;
border: 0;
border-bottom: 1px solid #ddd;
}
.markdown-body hr:before {
display: table;
content: "";
}
.markdown-body hr:after {
display: table;
clear: both;
content: "";
}
.markdown-body h1,
.markdown-body h2,
.markdown-body h3,
.markdown-body h4,
.markdown-body h5,
.markdown-body h6 {
margin-top: 15px;
margin-bottom: 15px;
line-height: 1.1;
}
.markdown-body h1 {
font-size: 30px;
}
.markdown-body h2 {
font-size: 21px;
}
.markdown-body h3 {
font-size: 16px;
}
.markdown-body h4 {
font-size: 14px;
}
.markdown-body h5 {
font-size: 12px;
}
.markdown-body h6 {
font-size: 11px;
}
.markdown-body blockquote {
margin: 0;
}
.markdown-body ul,
.markdown-body ol {
padding: 0;
margin-top: 0;
margin-bottom: 0;
}
.markdown-body ol ol,
.markdown-body ul ol {
list-style-type: lower-roman;
}
.markdown-body ul ul ol,
.markdown-body ul ol ol,
.markdown-body ol ul ol,
.markdown-body ol ol ol {
list-style-type: lower-alpha;
}
.markdown-body dd {
margin-left: 0;
}
.markdown-body code {
font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace;
font-size: 12px;
}
.markdown-body pre {
margin-top: 0;
margin-bottom: 0;
font: 12px Consolas, "Liberation Mono", Menlo, Courier, monospace;
}
.markdown-body .select::-ms-expand {
opacity: 0;
}
.markdown-body .octicon {
font: normal normal normal 16px/1 octicons-anchor;
display: inline-block;
text-decoration: none;
text-rendering: auto;
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
.markdown-body .octicon-link:before {
content: '\f05c';
}
.markdown-body:before {
display: table;
content: "";
}
.markdown-body:after {
display: table;
clear: both;
content: "";
}
.markdown-body>*:first-child {
margin-top: 0 !important;
}
.markdown-body>*:last-child {
margin-bottom: 0 !important;
}
.markdown-body a:not([href]) {
color: inherit;
text-decoration: none;
}
.markdown-body .anchor {
display: inline-block;
padding-right: 2px;
margin-left: -18px;
}
.markdown-body .anchor:focus {
outline: none;
}
.markdown-body h1,
.markdown-body h2,
.markdown-body h3,
.markdown-body h4,
.markdown-body h5,
.markdown-body h6 {
margin-top: 1em;
margin-bottom: 16px;
font-weight: bold;
line-height: 1.4;
}
.markdown-body h1 .octicon-link,
.markdown-body h2 .octicon-link,
.markdown-body h3 .octicon-link,
.markdown-body h4 .octicon-link,
.markdown-body h5 .octicon-link,
.markdown-body h6 .octicon-link {
color: #000;
vertical-align: middle;
visibility: hidden;
}
.markdown-body h1:hover .anchor,
.markdown-body h2:hover .anchor,
.markdown-body h3:hover .anchor,
.markdown-body h4:hover .anchor,
.markdown-body h5:hover .anchor,
.markdown-body h6:hover .anchor {
text-decoration: none;
}
.markdown-body h1:hover .anchor .octicon-link,
.markdown-body h2:hover .anchor .octicon-link,
.markdown-body h3:hover .anchor .octicon-link,
.markdown-body h4:hover .anchor .octicon-link,
.markdown-body h5:hover .anchor .octicon-link,
.markdown-body h6:hover .anchor .octicon-link {
visibility: visible;
}
.markdown-body h1 {
padding-bottom: 0.3em;
font-size: 2.25em;
line-height: 1.2;
border-bottom: 1px solid #eee;
}
.markdown-body h1 .anchor {
line-height: 1;
}
.markdown-body h2 {
padding-bottom: 0.3em;
font-size: 1.75em;
line-height: 1.225;
border-bottom: 1px solid #eee;
}
.markdown-body h2 .anchor {
line-height: 1;
}
.markdown-body h3 {
font-size: 1.5em;
line-height: 1.43;
}
.markdown-body h3 .anchor {
line-height: 1.2;
}
.markdown-body h4 {
font-size: 1.25em;
}
.markdown-body h4 .anchor {
line-height: 1.2;
}
.markdown-body h5 {
font-size: 1em;
}
.markdown-body h5 .anchor {
line-height: 1.1;
}
.markdown-body h6 {
font-size: 1em;
color: #777;
}
.markdown-body h6 .anchor {
line-height: 1.1;
}
.markdown-body p,
.markdown-body blockquote,
.markdown-body ul,
.markdown-body ol,
.markdown-body dl,
.markdown-body table,
.markdown-body pre {
margin-top: 0;
margin-bottom: 16px;
}
.markdown-body hr {
height: 4px;
padding: 0;
margin: 16px 0;
background-color: #e7e7e7;
border: 0 none;
}
.markdown-body ul,
.markdown-body ol {
padding-left: 2em;
}
.markdown-body ul ul,
.markdown-body ul ol,
.markdown-body ol ol,
.markdown-body ol ul {
margin-top: 0;
margin-bottom: 0;
}
.markdown-body li>p {
margin-top: 16px;
}
.markdown-body dl {
padding: 0;
}
.markdown-body dl dt {
padding: 0;
margin-top: 16px;
font-size: 1em;
font-style: italic;
font-weight: bold;
}
.markdown-body dl dd {
padding: 0 16px;
margin-bottom: 16px;
}
.markdown-body blockquote {
padding: 0 15px;
color: #777;
border-left: 4px solid #ddd;
}
.markdown-body blockquote>:first-child {
margin-top: 0;
}
.markdown-body blockquote>:last-child {
margin-bottom: 0;
}
.markdown-body table {
display: block;
width: 100%;
overflow: auto;
word-break: normal;
word-break: keep-all;
}
.markdown-body table th {
font-weight: bold;
}
.markdown-body table th,
.markdown-body table td {
padding: 6px 13px;
border: 1px solid #ddd;
}
.markdown-body table tr {
background-color: #fff;
border-top: 1px solid #ccc;
}
.markdown-body table tr:nth-child(2n) {
background-color: #f8f8f8;
}
.markdown-body img {
max-width: 100%;
box-sizing: content-box;
background-color: #fff;
}
.markdown-body code {
padding: 0;
padding-top: 0.2em;
padding-bottom: 0.2em;
margin: 0;
font-size: 85%;
background-color: rgba(0,0,0,0.04);
border-radius: 3px;
}
.markdown-body code:before,
.markdown-body code:after {
letter-spacing: -0.2em;
content: "\00a0";
}
.markdown-body pre>code {
padding: 0;
margin: 0;
font-size: 100%;
word-break: normal;
white-space: pre;
background: transparent;
border: 0;
}
.markdown-body .highlight {
margin-bottom: 16px;
}
.markdown-body .highlight pre,
.markdown-body pre {
padding: 16px;
overflow: auto;
font-size: 85%;
line-height: 1.45;
background-color: #f7f7f7;
border-radius: 3px;
}
.markdown-body .highlight pre {
margin-bottom: 0;
word-break: normal;
}
.markdown-body pre {
word-wrap: normal;
}
.markdown-body pre code {
display: inline;
max-width: initial;
padding: 0;
margin: 0;
overflow: initial;
line-height: inherit;
word-wrap: normal;
background-color: transparent;
border: 0;
}
.markdown-body pre code:before,
.markdown-body pre code:after {
content: normal;
}
.markdown-body kbd {
display: inline-block;
padding: 3px 5px;
font-size: 11px;
line-height: 10px;
color: #555;
vertical-align: middle;
background-color: #fcfcfc;
border: solid 1px #ccc;
border-bottom-color: #bbb;
border-radius: 3px;
box-shadow: inset 0 -1px 0 #bbb;
}
.markdown-body .pl-c {
color: #969896;
}
.markdown-body .pl-c1,
.markdown-body .pl-s .pl-v {
color: #0086b3;
}
.markdown-body .pl-e,
.markdown-body .pl-en {
color: #795da3;
}
.markdown-body .pl-s .pl-s1,
.markdown-body .pl-smi {
color: #333;
}
.markdown-body .pl-ent {
color: #63a35c;
}
.markdown-body .pl-k {
color: #a71d5d;
}
.markdown-body .pl-pds,
.markdown-body .pl-s,
.markdown-body .pl-s .pl-pse .pl-s1,
.markdown-body .pl-sr,
.markdown-body .pl-sr .pl-cce,
.markdown-body .pl-sr .pl-sra,
.markdown-body .pl-sr .pl-sre {
color: #183691;
}
.markdown-body .pl-v {
color: #ed6a43;
}
.markdown-body .pl-id {
color: #b52a1d;
}
.markdown-body .pl-ii {
background-color: #b52a1d;
color: #f8f8f8;
}
.markdown-body .pl-sr .pl-cce {
color: #63a35c;
font-weight: bold;
}
.markdown-body .pl-ml {
color: #693a17;
}
.markdown-body .pl-mh,
.markdown-body .pl-mh .pl-en,
.markdown-body .pl-ms {
color: #1d3e81;
font-weight: bold;
}
.markdown-body .pl-mq {
color: #008080;
}
.markdown-body .pl-mi {
color: #333;
font-style: italic;
}
.markdown-body .pl-mb {
color: #333;
font-weight: bold;
}
.markdown-body .pl-md {
background-color: #ffecec;
color: #bd2c00;
}
.markdown-body .pl-mi1 {
background-color: #eaffea;
color: #55a532;
}
.markdown-body .pl-mdr {
color: #795da3;
font-weight: bold;
}
.markdown-body .pl-mo {
color: #1d3e81;
}
.markdown-body kbd {
display: inline-block;
padding: 3px 5px;
font: 11px Consolas, "Liberation Mono", Menlo, Courier, monospace;
line-height: 10px;
color: #555;
vertical-align: middle;
background-color: #fcfcfc;
border: solid 1px #ccc;
border-bottom-color: #bbb;
border-radius: 3px;
box-shadow: inset 0 -1px 0 #bbb;
}
.markdown-body .plan-price-unit {
color: #767676;
font-weight: normal;
}
.markdown-body .task-list-item {
list-style-type: none;
}
.markdown-body .task-list-item+.task-list-item {
margin-top: 3px;
}
.markdown-body .task-list-item input {
margin: 0 0.35em 0.25em -1.6em;
vertical-align: middle;
}
.markdown-body .plan-choice {
padding: 15px;
padding-left: 40px;
display: block;
border: 1px solid #e0e0e0;
position: relative;
font-weight: normal;
background-color: #fafafa;
}
.markdown-body .plan-choice.open {
background-color: #fff;
}
.markdown-body .plan-choice.open .plan-choice-seat-breakdown {
display: block;
}
.markdown-body .plan-choice-free {
border-radius: 3px 3px 0 0;
}
.markdown-body .plan-choice-paid {
border-radius: 0 0 3px 3px;
border-top: 0;
margin-bottom: 20px;
}
.markdown-body .plan-choice-radio {
position: absolute;
left: 15px;
top: 18px;
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</style><title>README</title></head><body><article class="markdown-body"><h1>
<a id="user-content-sting" class="anchor" href="#sting" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>STing</h1>
<h4>
<a id="user-content-table-of-contents" class="anchor" href="#table-of-contents" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Table of contents:</h4>
<ul>
<li><a href="#requirements">Requirements</a></li>
<li><a href="#installation">Installation</a></li>
<li>
<a href="#quickstart-guide">Quickstart guide</a>
<ul>
<li><a href="#typing">Typing</a></li>
<li><a href="#gene-detection">Gene detection</a></li>
<li><a href="#preparing-the-database">Preparing the database:</a></li>
</ul>
</li>
<li><a href="#sting-applications">STing applications</a></li>
<li>
<a href="#sting-companion-scripts">STing companion scripts</a>
<ul>
<li><a href="#db_utilpy"><strong><code>db_util.py</code></strong></a></li>
<li><a href="#plot_kmer_depthr"><strong><code>plot_kmer_depth.R</code></strong></a></li>
</ul>
</li>
<li>
<a href="#using-sting">Using STing</a>
<ul>
<li><a href="#typing-mlst">Typing (MLST)</a></li>
<li><a href="#gene-detection-1">Gene Detection</a></li>
</ul>
</li>
<li>
<a href="#application-extended-help">Application extended help</a>
<ul>
<li><a href="#indexer">indexer</a></li>
<li><a href="#typer">typer</a></li>
</ul>
</li>
<li>
<a href="#seqan-version-211"><strong>SeqAn version:</strong> 2.1.1</a>
<ul>
<li><a href="#detector">detector</a></li>
</ul>
</li>
</ul>
<h2>
<a id="user-content-requirements" class="anchor" href="#requirements" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Requirements</h2>
<ul>
<li>Linux OS</li>
<li>gcc >= 4.8 and gcc <= 5.3
You may use gcc >= 5.3 to compile STing but you will see multiple warning messages. Those warning messages will not interfere with the binary generation.</li>
<li>autotols (Ubuntu: autotools)
<ul>
<li>Autoconf >= 2.69</li>
<li>Automake >= 1.15.1</li>
<li>Libtool >= 2.4.6</li>
</ul>
</li>
<li>autotools developer headers (Ubuntu: autotools-dev)</li>
<li>zlib >= 1.2.8 (Ubuntu: zlib)</li>
<li>zlib developer headers (Ubuntu: zlib1g-dev)</li>
</ul>
<h2>
<a id="user-content-installation" class="anchor" href="#installation" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Installation</h2>
<pre><code>./autogen.sh
./configure
make
make install
</code></pre>
<p>By default, <code>make install</code> will install all the files in <code>/usr/local/bin</code>, <code>/usr/local/lib</code> etc. You can specify an installation prefix other than <code>/usr/local</code> using the <code>--prefix</code> options from <code>./configure</code>, for instance <code>./configure --prefix=$HOME</code>. Please check all the available options of <code>./configure</code> by executing <code>./configure --help</code>.</p>
<h2>
<a id="user-content-quickstart-guide" class="anchor" href="#quickstart-guide" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Quickstart guide</h2>
<h3>
<a id="user-content-typing" class="anchor" href="#typing" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Typing</h3>
<p>Preparing directory:</p>
<pre><code>mkdir STing_demo
cd STing_demo
</code></pre>
<p>Downloading the <em>Neisseria spp.</em> MLST database from PubMLST.org and build a STing index from it:</p>
<pre><code>db_util.py fetch --query "Neisseria spp." --out_dir my_dbs --build_index
</code></pre>
<p>Downloading a WGS sample to analyze:</p>
<pre><code>wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_2.fastq.gz
</code></pre>
<p>Run STing typer:</p>
<pre><code>typer -x my_dbs/neisseria_spp/db/index -1 ERR026529_1.fastq.gz -2 ERR026529_2.fastq.gz -s ERR026529 -c -a -d -t ERR026529.depth.tsv -y -o ERR026529.results.tsv --sensitive
</code></pre>
<h3>
<a id="user-content-gene-detection" class="anchor" href="#gene-detection" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Gene detection</h3>
<p>Preparing directory:</p>
<pre><code>mkdir -p STing_demo/my_dbs/card
cd STing_demo/my_dbs/card
</code></pre>
<h3>
<a id="user-content-preparing-the-database" class="anchor" href="#preparing-the-database" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Preparing the database:</h3>
<p>Downloading the antimicrobial resistance gene database from <a href="https://card.mcmaster.ca/" rel="nofollow">CARD</a></p>
<pre><code>wget https://card.mcmaster.ca/latest/data -O card.tgz
tar xvf card.tgz
</code></pre>
<p>Changing IUPAC extended DNA characters to N on the CARD nucleotide file:</p>
<pre><code>sed -e '/^[^>]/s/[^ATGCatgc]/N/g' nucleotide_fasta_protein_homolog_model.fasta > card.fasta
</code></pre>
<p>Creating STing db config file:</p>
<pre><code>echo -e "[loci]\ncard\tcard.fasta\n" > config.txt
</code></pre>
<p>The new config file should look like this:</p>
<pre><code>[loci]
card card.fasta
</code></pre>
<p>Creating the STing database index:</p>
<pre><code>indexer -c config.txt -p db/index -m GDETECT
</code></pre>
<p>Downloading a WGS sample to analyze:</p>
<pre><code>wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_2.fastq.gz
</code></pre>
<p>Run STing detector:</p>
<pre><code>cd ../../
typer -x my_dbs/neisseria_spp/db/index -1 ERR026529_1.fastq.gz -2 ERR026529_2.fastq.gz -s ERR026529 -c -a -d -t ERR026529.depth.tsv -y -o ERR026529.results.tsv --sensitive
</code></pre>
<h2>
<a id="user-content-sting-applications" class="anchor" href="#sting-applications" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>STing applications</h2>
<p>STing has three applications:</p>
<ul>
<li>
<p><strong><code>indexer</code></strong>
: Creates the indexes (databases) required to execute a locus-based typing analysis and detect genes.</p>
</li>
<li>
<p><strong><code>typer</code></strong>
: Predicts STs of a read sample based on an index built from a species-specific locus-based typing scheme (allelic profile table and sequences of observed alleles).</p>
</li>
<li>
<p><strong><code>detector</code></strong>
: Detects genes in a read sample based on an index built from sequences of a set of genes of interest.</p>
</li>
</ul>
<p>To explore the usage and available options for each tool, run the corresponding application using the option <code>-h</code> or <code>--help</code>:</p>
<pre><code>indexer -h
typer -h
detector -h
</code></pre>
<h2>
<a id="user-content-sting-companion-scripts" class="anchor" href="#sting-companion-scripts" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>STing companion scripts</h2>
<p>STing includes two companion scripts:</p>
<h3>
<a id="user-content-db_utilpy" class="anchor" href="#db_utilpy" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong><code>db_util.py</code></strong>
</h3>
<p>This script provides a set of utilities to download databases from PubMLST and build STing indices from them.</p>
<pre><code>
This script provides a set of utilities to download databases from PubMLST and build STing indices from them.
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
subcommands:
{list,query,fetch}
list List all the available databases at PubMLST
query Search a database in PubMLST
fetch Fetch a database from PubMLST
</code></pre>
<p>To list the available MLST schemes and their last update time, use the <code>list</code> sub-command:</p>
<div class="highlight highlight-source-shell"><pre>./scripts/db_util.py list
<span class="pl-c"><span class="pl-c">#</span> # Database #Profiles Retrieved DB_URL</span>
<span class="pl-c"><span class="pl-c">#</span> 1 Achromobacter spp. 476 2019-11-18 https://pubmlst.org/achromobacter</span>
<span class="pl-c"><span class="pl-c">#</span> 2 Acinetobacter baumannii#1 2058 2019-11-18 https://pubmlst.org/abaumannii/</span>
</pre></div>
<p>To search the available PubMLST schemes by search term (e.g. 'cholera'), use the <code>query</code> sub-command:</p>
<div class="highlight highlight-source-shell"><pre>./scripts/db_util.py query <span class="pl-s"><span class="pl-pds">"</span>cholera<span class="pl-pds">"</span></span>
<span class="pl-c"><span class="pl-c">#</span> 1 -b 984 2019-11-18 https://pubmlst.org/vcholerae/</span>
<span class="pl-c"><span class="pl-c">#</span> 2 Vibrio cholerae#2 422 2019-11-18 http://pubmlst.org/vcholerae</span></pre></div>
<p>Finally, to download and build a PubMLST database, use the <code>fetch</code> sub-command:</p>
<div class="highlight highlight-source-shell"><pre>./scripts/db_util.py fetch -q <span class="pl-s"><span class="pl-pds">"</span>Vibrio cholerae<span class="pl-pds">"</span></span> -b -o testdb
<span class="pl-c"><span class="pl-c">#</span> Database: "Vibrio cholerae"</span>
<span class="pl-c"><span class="pl-c">#</span> Fetching allele sequences:</span>
<span class="pl-c"><span class="pl-c">#</span> - https://pubmlst.org/data/alleles/vcholerae/adk.tfa -> /storage/aroon/sting/databases/vibrio_cholerae/adk.fa</span>
<span class="pl-c"><span class="pl-c">#</span> - https://pubmlst.org/data/alleles/vcholerae/gyrB.tfa -> /storage/aroon/sting/databases/vibrio_cholerae/gyrB.fa</span>
<span class="pl-c"><span class="pl-c">#</span> - https://pubmlst.org/data/alleles/vcholerae/mdh.tfa -> /storage/aroon/sting/databases/vibrio_cholerae/mdh.fa</span>
<span class="pl-c"><span class="pl-c">#</span> - https://pubmlst.org/data/alleles/vcholerae/metE.tfa -> /storage/aroon/sting/databases/vibrio_cholerae/metE.fa</span>
<span class="pl-c"><span class="pl-c">#</span> - https://pubmlst.org/data/alleles/vcholerae/pntA.tfa -> /storage/aroon/sting/databases/vibrio_cholerae/pntA.fa</span>
<span class="pl-c"><span class="pl-c">#</span> - https://pubmlst.org/data/alleles/vcholerae/purM.tfa -> /storage/aroon/sting/databases/vibrio_cholerae/purM.fa</span>
<span class="pl-c"><span class="pl-c">#</span> - https://pubmlst.org/data/alleles/vcholerae/pyrC.tfa -> /storage/aroon/sting/databases/vibrio_cholerae/pyrC.fa</span>
<span class="pl-c"><span class="pl-c">#</span> Fetching profiles:</span>
<span class="pl-c"><span class="pl-c">#</span> - https://pubmlst.org/data/profiles/vcholerae.txt -> /storage/aroon/sting/databases/vibrio_cholerae/profile.txt</span>
<span class="pl-c"><span class="pl-c">#</span> Building STing index:</span>
<span class="pl-c"><span class="pl-c">#</span> /data/home/achande3/bin/indexer -c /storage/aroon/sting/databases/vibrio_cholerae/config.txt -p /storage/aroon/sting/databases/vibrio_cholerae/db/index</span>
<span class="pl-c"><span class="pl-c">#</span> Loading sequences from sequences files:</span>
<span class="pl-c"><span class="pl-c">#</span> # Seqs. File</span>
<span class="pl-c"><span class="pl-c">#</span> 1 130 /storage/aroon/sting/databases/vibrio_cholerae/adk.fa</span>
<span class="pl-c"><span class="pl-c">#</span> 2 151 /storage/aroon/sting/databases/vibrio_cholerae/gyrB.fa</span>
<span class="pl-c"><span class="pl-c">#</span> 3 164 /storage/aroon/sting/databases/vibrio_cholerae/mdh.fa</span>
<span class="pl-c"><span class="pl-c">#</span> 4 329 /storage/aroon/sting/databases/vibrio_cholerae/metE.fa</span>
<span class="pl-c"><span class="pl-c">#</span> 5 185 /storage/aroon/sting/databases/vibrio_cholerae/pntA.fa</span>
<span class="pl-c"><span class="pl-c">#</span> 6 128 /storage/aroon/sting/databases/vibrio_cholerae/purM.fa</span>
<span class="pl-c"><span class="pl-c">#</span> 7 259 /storage/aroon/sting/databases/vibrio_cholerae/pyrC.fa</span>
<span class="pl-c"><span class="pl-c">#</span> Total loaded sequences: 1346</span>
<span class="pl-c"><span class="pl-c">#</span> Creating and saving ESA index from loaded sequences...</span>
<span class="pl-c"><span class="pl-c">#</span> Index successfuly created!</span>
</pre></div>
<h3>
<a id="user-content-plot_kmer_depthr" class="anchor" href="#plot_kmer_depthr" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong><code>plot_kmer_depth.R</code></strong>
</h3>
<p>This script Generates <strong>k</strong>-mer depth plots from output depth files generated by the <code>typer</code> and <code>detector</code> applications.</p>
<h4>
<a id="user-content-requirements-1" class="anchor" href="#requirements-1" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Requirements:</h4>
<p><code>plot_kmer_depth.R</code> requires the following R packages:</p>
<ul>
<li>argparser</li>
<li>ggsci</li>
<li>gridExtra</li>
<li>RColorBrewer</li>
<li>stringr</li>
<li>svglite</li>
<li>tidyverse</li>
</ul>
<p>By default, <code>plot_kmer_depth.R</code> will try to install automatically the required packages to the personal R library directory (usually something like <code>~/R/x86_64-pc-linux-gnu-library/3.4</code>).</p>
<pre><code> ./scripts/plot_kmer_depth.R
usage: plot_kmer_depth.R [--] [--help] [--opts OPTS] [--gene_file GENE_FILE] [--prefix PREFIX] [--sample_name SAMPLE_NAME] [--max_loci_per_page MAX_LOCI_PER_PAGE] [--format FORMAT] input_file
This script generates k-mer depth plots using a depth file generated by the STing typer tool (-t option).
positional arguments:
input_file Samples file. Text file with a list of sample names (line by line).
flags:
-h, --help show this help message and exit
optional arguments:
-x, --opts OPTS RDS file containing argument values
-g, --gene_file GENE_FILE Path to a text file with a list of genes/loci to be plotted.
-p, --prefix PREFIX Filename prefix for output files. [default: kmer_depth]
-s, --sample_name SAMPLE_NAME Sample name. [default: input file's name]
-m, --max_loci_per_page MAX_LOCI_PER_PAGE Maximum number of loci to print on each page. [default: 7]
-f, --format FORMAT Output file format. Valid options are 'pdf', 'png', and 'svg' [default: pdf]
</code></pre>
<h2>
<a id="user-content-using-sting" class="anchor" href="#using-sting" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Using STing</h2>
<p>Next subsections present a brief description of the MLST analysis and gene detection workflows of STing. For the detailed help and usage of each application, please check the last section of this document (<a href="#extended-help-of-the-applications">Application extended help</a>).
In order to test the different STing tools, the folder <code>test</code> is included at the STing root directory. It contains the example files described below (configuration, profiles, and sequences) in addition to some read samples.</p>
<h3>
<a id="user-content-typing-mlst" class="anchor" href="#typing-mlst" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Typing (MLST)</h3>
<p>Two main steps are required to execute an MLST analysis with STing: <em>Database indexing</em> and <em>ST prediction</em></p>
<h4>
<a id="user-content-database-indexing" class="anchor" href="#database-indexing" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Database indexing</h4>
<ol>
<li>
<p>Create a config file that contains the path to loci and allelic profiles files. The format details for each file are the following:</p>
<h5>
<a id="user-content-config-file" class="anchor" href="#config-file" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Config file</h5>
<p>A tab separated file that follows this format:</p>
<pre><code>[loci]
locus1 relative/path/to/locusFile1.fa
locus2 relative/path/to/locusFile2.fa
[profile]
profile relative/path/to/profileFile.txt
</code></pre>
<p>Blank lines and comments (lines starting with <code>#</code>) in this file, will be ignored. Paths are relative to the config file itself.
This is an example of a configuration file for the species <em>Neisseria spp.</em> (<code>test/mlst/pubmlst_db_files/Neisseria_spp/config.txt</code>):</p>
<pre><code>[loci]
abcZ abcZ.fa
adk adk.fa
aroE aroE.fa
fumC fumC.fa
gdh gdh.fa