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_sources/intro.md

@@ -5,6 +5,19 @@ metagenome assembly and analysis as part of the microbiome multi-omics data scie
 MOSHPIT enables flexible, modular, fully reproducible workflows for read-based or assembly-based analysis of 
 metagenome data.
 
+The following main plugins comprise the core of the MOSHPIT suite:
+- [q2-assembly](https://github.com/bokulich-lab/q2-assembly): contains actions for (meta)genome and quality control, 
+    genome indexing and red mapping
+- [q2-moshpit](https://github.com/bokulich-lab/q2-moshpit): provides actions for contig binning and quality control, 
+    taxonomic and functional annotations of contigs and MAGs, human host removal.
+
+Additionally, you may want to check out our plugins for AMR genes detection and viromics applications (they are not 
+covered in this tutorial but you may use them with some of the artifacts produced by the MOSHPIT plugins):
+- [q2-rgi](https://github.com/bokulich-lab/q2-rgi): antimicrobial resistance gene annotation of MAGs and metagenomic 
+    reads with RGI and CARD
+- [q2-amrfinderplus](https://github.com/bokulich-lab/q2-amrfinderplus): AMR detection using the AMRFinderPlus tool
+- [q2-viromics](https://github.com/bokulich-lab/q2-viromics): detection of viral sequences and their quality control.
+
 This tutorial will guide you through the process of analyzing metagenomic data using QIIME 2 framework and MOSHPIT. 
 The tutorial is divided into several chapters, each focusing on a different aspect of metagenomic data analysis. 
 We will use a small published dataset to demonstrate the capabilities of most of the methods available in MOSHPIT.

intro.html

@@ -333,6 +333,21 @@ <h1>MOSHPIT tutorial<a class="headerlink" href="#moshpit-tutorial" title="Link t
 metagenome assembly and analysis as part of the microbiome multi-omics data science platform <a class="reference external" href="https://qiime2.org/">QIIME 2</a>.
 MOSHPIT enables flexible, modular, fully reproducible workflows for read-based or assembly-based analysis of
 metagenome data.</p>
+<p>The following main plugins comprise the core of the MOSHPIT suite:</p>
+<ul class="simple">
+<li><p><a class="reference external" href="https://github.com/bokulich-lab/q2-assembly">q2-assembly</a>: contains actions for (meta)genome and quality control,
+genome indexing and red mapping</p></li>
+<li><p><a class="reference external" href="https://github.com/bokulich-lab/q2-moshpit">q2-moshpit</a>: provides actions for contig binning and quality control,
+taxonomic and functional annotations of contigs and MAGs, human host removal.</p></li>
+</ul>
+<p>Additionally, you may want to check out our plugins for AMR genes detection and viromics applications (they are not
+covered in this tutorial but you may use them with some of the artifacts produced by the MOSHPIT plugins):</p>
+<ul class="simple">
+<li><p><a class="reference external" href="https://github.com/bokulich-lab/q2-rgi">q2-rgi</a>: antimicrobial resistance gene annotation of MAGs and metagenomic
+reads with RGI and CARD</p></li>
+<li><p><a class="reference external" href="https://github.com/bokulich-lab/q2-amrfinderplus">q2-amrfinderplus</a>: AMR detection using the AMRFinderPlus tool</p></li>
+<li><p><a class="reference external" href="https://github.com/bokulich-lab/q2-viromics">q2-viromics</a>: detection of viral sequences and their quality control.</p></li>
+</ul>
 <p>This tutorial will guide you through the process of analyzing metagenomic data using QIIME 2 framework and MOSHPIT.
 The tutorial is divided into several chapters, each focusing on a different aspect of metagenomic data analysis.
 We will use a small published dataset to demonstrate the capabilities of most of the methods available in MOSHPIT.</p>