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@@ -1096,6 +1098,12 @@ <h2 id="pipeline-tools">Pipeline tools</h2>
 </blockquote>
 </li>
 <li>
+<p><a href="https://humid.readthedocs.io/en/latest/usage.html">HUMID</a></p>
+<blockquote>
+<p>Laros J, van den Berg R, <strong>Github</strong> https://github.com/jfjlaros/HUMID</p>
+</blockquote>
+</li>
+<li>
 <p><a href="https://www.ncbi.nlm.nih.gov/pubmed/30621750/">iVar</a></p>
 <blockquote>
 <p>Grubaugh, Nathan D et al. “An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.” Genome biology vol. 20,1 8. 8 Jan. 2019, doi:10.1186/s13059-018-1618-7</p>
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latest/index.html

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@@ -907,6 +909,7 @@ <h2 id="pipeline-summary">Pipeline summary</h2>
 <li>Read QC (<a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"><code>FastQC</code></a>)</li>
 <li>Performs optional read pre-processing<ul>
 <li>Adapter trimming(<a href="https://github.com/OpenGene/fastp"><code>fastp</code></a>, <a href="https://github.com/usadellab/Trimmomatic"><code>Trimmomatic</code></a>)</li>
+<li>Read UMI deduplication (<a href="https://humid.readthedocs.io/en/latest/usage.html"><code>HUMID</code></a>)</li>
 <li>Low complexity and quality filtering (<a href="https://jgi.doe.gov/data-and-tools/software-tools/bbtools/"><code>bbduk</code></a>)</li>
 <li>Host-read removal (<a href="http://bowtie-bio.sourceforge.net/bowtie2/"><code>BowTie2</code></a>)</li>
 </ul>
@@ -988,11 +991,7 @@ <h2 id="contributions-and-support">Contributions and Support</h2>
 -->
 
 <h2 id="citations">Citations</h2>
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-
-<!-- If you use  Joon-Klaps/viralgenie for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
-
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+<!-- TODO: If you use  Joon-Klaps/viralgenie for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
 <p>An extensive list of references for the tools used by the pipeline can be found in the <a href="https://github.io/Joon-klaps/viralgenie/CITATIONS"><code>CITATIONS.md</code></a> file.</p>
 <p>You can cite the <code>nf-core</code> publication as follows:</p>
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latest/installation/index.html

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latest/javascripts/katex.js

@@ -0,0 +1,10 @@
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latest/output/index.html

@@ -50,6 +50,8 @@
 
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@@ -582,6 +584,15 @@
     </span>
   </a>
 
+</li>
+
+          <li class="md-nav__item">
+  <a href="#umi-deduplication" class="md-nav__link">
+    <span class="md-ellipsis">
+      UMI-deduplication
+    </span>
+  </a>
+
 </li>
 
           <li class="md-nav__item">
@@ -1382,6 +1393,15 @@
     </span>
   </a>
 
+</li>
+
+          <li class="md-nav__item">
+  <a href="#umi-deduplication" class="md-nav__link">
+    <span class="md-ellipsis">
+      UMI-deduplication
+    </span>
+  </a>
+
 </li>
 
           <li class="md-nav__item">
@@ -1855,6 +1875,28 @@ <h3 id="trimmomatic">Trimmomatic</h3>
 </ul>
 </details>
 <p>By default viralgenie will only provide the report and log files if Trimmomatic is selected. The trimmed reads can be saved by specifying <code>--save_intermediate_reads</code> or <code>--save_final_reads 'trimming'</code>.</p>
+<h3 id="umi-deduplication">UMI-deduplication</h3>
+<p>UMI-deduplication can be done at the read level using <a href="https://humid.readthedocs.io/en/latest/usage.html"><code>HUMID</code></a>. Viralgenie also uses provides the opportunity to extract the UMI from the read using <a href="https://umi-tools.readthedocs.io/en/latest/QUICK_START.html#step-3--extract-the-umis"><code>UMI-tools extract</code></a> if the UMI is not in the header. Results will be stored in the <code>preprocessing/umi</code> directory.</p>
+<details class="- abstract">
+<summary>Output files</summary>
+<ul>
+<li><code>umi/</code><ul>
+<li><code>humid/</code><ul>
+<li><code>log/&lt;sample-id&gt;.log</code>: log file of humid.</li>
+<li><code>annotated/&lt;sample-id&gt;_annotated_*.fastq.gz</code>: annotated FastQ files, reads will have their assigned cluster in the read header.</li>
+<li><code>deduplicated/&lt;sample-id&gt;_deduplicated_*.fastq.gz</code>: deduplicated FastQ files.</li>
+</ul>
+</li>
+<li><code>umitools/</code><ul>
+<li><code>log/&lt;sample-id&gt;.log</code>: log file of umi-tools.</li>
+<li><code>extracts/&lt;sample-id&gt;.umi_extract*.fastq.gz</code>: fastq file where UMI's have been removed from the read and moved to the read header.</li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+</details>
+<p>By default viralgenie will not assume reads have UMI's. To enable this use the parameter <code>--with_umi</code>. Specify where UMI deduplication should occur with <code>--umi_deduplicate</code> if at a <code>read</code> level, on a <code>mapping</code> level or <code>both</code> at a read and mapping level. The deduplicated reads can be saved by specifying <code>--save_intermediate_reads</code> or <code>--save_final_reads 'deduplication'</code>.</p>
 <h3 id="bbduk">BBDuk</h3>
 <p><a href="https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/">BBDuk</a> stands for Decontamination Using Kmers. BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single high-performance tool.</p>
 <p>It is used in viralgenie for complexity filtering using different algorithms. This means that it will remove reads with low sequence diversity (e.g. mono- or dinucleotide repeats).</p>
@@ -2032,7 +2074,6 @@ <h3 id="clustering">Clustering</h3>
 <summary>Output files</summary>
 <ul>
 <li><code>polishing/intermediate/cluster/</code><ul>
-<li><code>&lt;sample-id&gt;/&lt;sample-id&gt;_cl#.json</code>: A json file containign information that is used by viralgenie internally like clusterID, centroid, members, cluster size, if the reference is external or a denovo contig.</li>
 <li><code>&lt;sample-id&gt;/&lt;sample-id&gt;.summary_mqc.tsv</code>: A tabular file with comments used for <a href="#multiqc">Multiqc</a> with statistics on the number of identified clusters in a sample</li>
 <li><code>&lt;sample-id&gt;/&lt;sample-id&gt;.clusters.tsv</code>: A tabular file with metadata on all clusters in a samples. It's the json file of all clusters in a table format.</li>
 </ul>
@@ -2883,6 +2924,12 @@ <h4>Cookie Consent</h4>
 
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latest/parameters/index.html

@@ -50,6 +50,8 @@
 
       <link rel="stylesheet" href="../stylesheets/extra.css">
 
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@@ -1134,7 +1136,7 @@ <h2 id="inputoutput-options">Input/output options</h2>
 <tbody>
 <tr>
 <td><code>input</code></td>
-<td>Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See <a href="https://nf-co.re/viralgenie/usage#samplesheet-input">usage docs</a>.</small></details></td>
+<td>Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See <a href="https://joon-klaps.github.io/viralgenie/latest/usage/#input">usage docs</a>.</small></details></td>
 <td></td>
 </tr>
 <tr>
@@ -1196,8 +1198,28 @@ <h2 id="preprocessing-options">Preprocessing options</h2>
 <td>True</td>
 </tr>
 <tr>
+<td><code>umi_deduplicate</code></td>
+<td>Specify at what level UMI deduplication should occur.</td>
+<td>read</td>
+</tr>
+<tr>
+<td><code>humid_mismatches</code></td>
+<td>Specify the maximum number of mismatches between reads for them to still be considered neighbors.</td>
+<td>1</td>
+</tr>
+<tr>
+<td><code>humid_strategy</code></td>
+<td>Specify the strategy for umi-deduplication directional vs cluster</td>
+<td>directional</td>
+</tr>
+<tr>
+<td><code>umitools_dedup_strategy</code></td>
+<td>Specify the strategy or method for umi-tools deduplication on mapping level</td>
+<td>directional</td>
+</tr>
+<tr>
 <td><code>umi_discard_read</code></td>
-<td>Discard R1 / R2 if required</td>
+<td>Discard R1 / R2 if required 0, meaning not to discard</td>
 <td>0</td>
 </tr>
 <tr>
@@ -1268,7 +1290,7 @@ <h2 id="preprocessing-options">Preprocessing options</h2>
 <tr>
 <td><code>skip_host_fastqc</code></td>
 <td>Skip the fastqc step after host &amp; contaminants were removed</td>
-<td>True</td>
+<td></td>
 </tr>
 </tbody>
 </table>
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