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@@ -159,6 +159,26 @@ <h2 id="quick-start">Quick Start</h2>
   --id_mapping id_mapping_file \
   -profile &lt;docker/singularity/podman/shifter/charliecloud/conda/institute&gt;
 </code></pre>
+<h2 id="databases-and-references">Databases and references</h2>
+<p>A question that pops up a lot is: Since Euryale requires a lot of reference parameters, where can I find these references?</p>
+<p>Below we provide a short list of places where you can find these databases.
+But, of course, we're not limited to these references: Euryale should be able to process your own databases, should you want to build them yourself.</p>
+<h3 id="alignment">Alignment</h3>
+<p>For the alignment you can either provide <code>--diamond_db</code> for a pre-built DIAMOND database, or you can provide <code>--reference_fasta</code>.
+For reference fasta, by default Euryale expects something like <a href="https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/">NCBI-nr</a>, but similarly formatted reference databases should also suffice.</p>
+<h3 id="taxonomic-classification_1">Taxonomic classification</h3>
+<p>At its current version, Euryale doesn't build a reference taxonomic database, but pre-built ones are supported.</p>
+<ul>
+<li>If you're using Kaiju (the default), you can provide a reference database with <code>--kaiju_db</code> and provide a .tar.gz file like the ones provided in the <a href="https://kaiju.binf.ku.dk/server">official Kaiju website</a>.
+  We have extensively tested Euryale with the 2021 version of the nr database and it should work as expected.</li>
+<li>If you're using Kraken2 (By supplying <code>--run_kraken2</code>), we expect something like the <a href="https://benlangmead.github.io/aws-indexes/k2">pre-built .tar.gz databases provided by the Kraken2 developers</a> to be provided to <code>--kraken2_db</code>.</li>
+</ul>
+<h3 id="functional-annotation_1">Functional annotation</h3>
+<p>We expect an ID mapping reference to be used within annotate. Since we're already expecting by default the NCBI-nr to be used as the alignment reference, <a href="https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/">the ID mapping data file provided by Uniprot</a> should work well when provided to <code>--id_mapping</code>.</p>
+<h3 id="host-reference">Host reference</h3>
+<p>If you're using metagenomic reads that come from a known host's microbiome, you can also provide the host's genome FASTA to <code>--host_fasta</code> parameter in order to enable our decontamination subworkflow.
+<a href="https://www.ensembl.org/index.html">Ensembl</a> provides easy to download genomes that can be used for this purpose.
+Alternatively, you can provide a pre-built BowTie2 database directory to the <code>--bowtie2_db</code> parameter.</p>
 <h2 id="documentation">Documentation</h2>
 <p>The dalmolingroup/euryale documentation is split into the following pages:</p>
 <ul>
@@ -246,5 +266,5 @@ <h2 id="citations">Citations</h2>
 
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