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<div id="header">
<h1 class="title toc-ignore">Installing genomes and variations from
Ensembl</h1>
<h4 class="author">Jacques van Helden</h4>
<h4 class="date">2024-05-20</h4>
</div>
<div id="rsat-tools-to-install-genomes-from-ensembl"
class="section level1" number="1">
<h1><span class="header-section-number">1</span> RSAT tools to install
genomes from Ensembl</h1>
<p>The Ensembl browser (<a href="http://ensembl.org"
class="uri">http://ensembl.org</a>) contains mostly genomes of
Vertebrate organisms.</p>
<p>RSAT includes a series of programs to download and install genomes
from Ensembl:</p>
<ol style="list-style-type: decimal">
<li><p><code>install-ensembl-genome</code> is a wrapper enabling to
autmoatize the download (genome sequences, features, variations) and
configuration tasks.</p></li>
<li><p><code>download-ensembl-genome</code> downloads the genomics
sequences and converts them in the raw format required for .</p></li>
<li><p><code>download-ensembl-features</code> downloads tab-delimited
text files describing genomic features (transcripts, CDS, genes,
…).</p></li>
<li><p><code>download-ensembl-variations</code> downloads tab-delimited
text files describing genomic variations (polymorphism).</p></li>
</ol>
</div>
<div id="installing-genomes-from-ensembl" class="section level1"
number="2">
<h1><span class="header-section-number">2</span> Installing genomes from
Ensembl</h1>
<p>The program <code>install-ensembl-genome</code> manages all the
required steps to download and install a genome (sequence, features, and
optionally variations) from Ensembl to <em>RSAT</em>.</p>
<p>It performs the following tasks:</p>
<ol style="list-style-type: decimal">
<li><p><code>install-ensembl-genome -available_species</code> returns
the list species available on the Ensembl server, together with their
status of availability for the 3 data types (genome sequence, features,
variations). When thisoption is called, the program does not install any
genome.</p></li>
<li><p>The option
<code>install-ensembl-genome -task genome -org [Selected_organism]</code>
runs the program <code>download-ensembl-genome</code> to download the
complete genomic sequence of a given organism from the <a
href="http://ensembl.org">Ensembl Web site</a>, and formats it according
to <em>RSAT</em> requirements (conversion from the original fasta
sequence file to one file per chromosome, in raw format).</p></li>
<li><p>The option
<code>install-ensembl-genome -task features -org [Selected_organism]</code>
runs <code>download-ensembl-features</code> to download the positions
and descriptions of genomic features (genes, CDS, mRNAs, …).</p></li>
<li><p>If the option <code>-task variations</code> is activated,
<code>install-ensembl-genome -org [Selected_organism]</code> runs
<code>download-ensembl-variations</code> to download the description of
genomic variations (polymorphism). Note that variations are supported
only for a subset of genomes.</p></li>
<li><p><code>install-ensembl-genome -org [Selected_organism] -task config</code>
updates RSAT configuration files to make the newly installed genome
available.</p></li>
<li><p><code>install-ensembl-genome -org [Selected_organism] -task install</code>
runs the additional tasks required to have a fully functional genome on
the local site: compute genomic statisics (intergenic sizes, …) and
background models (oligonucleotide and dyad frequencies).</p></li>
</ol>
<p>The detailed description of the program and the list of options can
be obtained with the option .</p>
<div class="sourceCode" id="cb1"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="co">## Get the description of the program + all options</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="ex">install-ensembl-genome</span> <span class="at">-help</span></span></code></pre></div>
</div>
<div id="getting-the-list-of-available-genomes" class="section level1"
number="3">
<h1><span class="header-section-number">3</span> Getting the list of
available genomes</h1>
<p>Before installing a genome, it is generally a good idea to know which
genomes are available. For this, use the option .</p>
<div class="sourceCode" id="cb2"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="bu">export</span> <span class="va">TODAY</span><span class="op">=</span><span class="kw">`</span><span class="fu">date</span> <span class="st">'+%Y-%m-%d'</span><span class="kw">`</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a></span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a><span class="co">## Retrieve the list of supported species on EnsEMBL</span></span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a><span class="ex">install-ensembl-genome</span> <span class="at">-v</span> 1 <span class="at">-available_species</span> <span class="dt">\</span></span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a> <span class="at">-o</span> available_species_ensembl_<span class="va">${TODAY}</span>.tsv</span>
<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a> </span>
<span id="cb2-7"><a href="#cb2-7" tabindex="-1"></a><span class="co">## Read the result file</span></span>
<span id="cb2-8"><a href="#cb2-8" tabindex="-1"></a><span class="fu">more</span> available_species_ensembl_<span class="va">${TODAY}</span>.tsv</span>
<span id="cb2-9"><a href="#cb2-9" tabindex="-1"></a></span>
<span id="cb2-10"><a href="#cb2-10" tabindex="-1"></a><span class="co">## Count the number of available genomes (using grep -v to discard comment lines)</span></span>
<span id="cb2-11"><a href="#cb2-11" tabindex="-1"></a><span class="fu">grep</span> <span class="at">-v</span> <span class="st">'^;'</span> available_species_ensembl_<span class="va">${TODAY}</span>.tsv <span class="kw">|</span> <span class="fu">wc</span> <span class="at">-l</span></span>
<span id="cb2-12"><a href="#cb2-12" tabindex="-1"></a><span class="co">## Note: on August 6, 2018, this returns 117 organism names</span></span></code></pre></div>
</div>
<div id="availability-of-polymorphic-variations-for-genomes-in-ensembl"
class="section level1" number="4">
<h1><span class="header-section-number">4</span> Availability of
polymorphic variations for genomes in Ensembl</h1>
<p><strong><em>Beware:</em></strong> inter-individual variations are
available for a subset only of the genomes available in Ensembl. The
option <code>-available_species</code> indicates, for each species, the
availability (genome, features, variations). Obviously, the programs to
analyse regulatory variations (<code>variation-info</code>,
<code>convert-variations</code>, <code>retrieve-variation-seq</code>,
<code>variation-scan</code>) are working only for the genomes documented
with variations.</p>
<div class="sourceCode" id="cb3"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="co">## select genomes for which variations are available in Ensembl</span></span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="fu">awk</span> <span class="at">-F</span><span class="st">'\t'</span> <span class="st">'$2 ~ "variations"'</span> available_species_ensembl_<span class="va">${TODAY}</span>.tsv <span class="kw">|</span> <span class="fu">grep</span> <span class="at">-v</span> <span class="st">'^;'</span></span></code></pre></div>
</div>
<div id="installing-a-genome-from-ensembl" class="section level1"
number="5">
<h1><span class="header-section-number">5</span> Installing a genome
from Ensembl</h1>
<p>We can now download and install the complete genomic sequence for the
species of our choice. For the sake of space and time economy, we will
use a small genome for this manual: the budding yeast <em>Saccharomyces
cerevisiae</em>.</p>
<p><em>Beware</em>: some installation steps take a lot of time. For
large genomes (e.g. Vertebrate organisms), the full installation can
thus take several hours. This should in principle not be a big issue,
since installing a genome is not a daily task, but it is worth knowing
that the whole process requires a continuous connection during several
hours.</p>
<div class="sourceCode" id="cb4"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="co">## Install the genome sequences for a selected organism</span></span>
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="ex">install-ensembl-genome</span> <span class="at">-v</span> 2 <span class="at">-species</span> Saccharomyces_cerevisiae</span></code></pre></div>
<p>This command will automatically run all the installation tasks
described above, except the installation of variations (see Section <a
href="#sect:download_ensembl_variations">1.3</a>).</p>
<!--
# Installing genomes from EnsemblGenomes
The historical Ensembl project was focused on vertebrate genomes + a few model organisms (, , …).
A more recent project called extends the project to a wider taxonomic range (in August 2018, EnsemblGenomes release 40 contains 45175 genomes, where as Ensembl only provides 117 genomes).
The program `install-ensembl-genome` supports the installation of genomes from EnsemblGenomes as well as Ensembl. By default, it opens a connection to the historical Ensembl database, but the option `-db ensemblgenomes` enables to install genomes from EnsemblGenomes.
```bash
export TODAY=`date '+%Y-%m-%d'`
## Get the list of available species from the extended project
## EnsemblGenomes
install-ensembl-genome -v 2 -available_species -db ensemblgenomes \
-o available_species_EnsemblGenome_${TODAY}.tsv
## Count the number of genomes available
grep -v '^;' available_species_EnsemblGenome_${TODAY}.tsv | wc -l
## Returns 45175 on August 6, 2018
```
You can then identify your genome of interest in the file , and start the installation (don’t forget the option .
```bash
## Install Escherichia coli (strain K12 MG1665) from EnsemblGenomes
install-ensembl-genome -v 2 -db ensemblgenomes \
-species Escherichia_coli_str_k_12_substr_mg1655
```
-->
</div>
<div id="downloading-variations" class="section level1" number="6">
<h1><span class="header-section-number">6</span> Downloading
variations</h1>
<p>The program downloads variations from the Web site, and installs it
on the local site.</p>
<p>This program relies on , which must be installed beforehand on your
computer.</p>
<div class="sourceCode" id="cb5"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="co">## Retrieve the list of supported species in the EnsEMBL variation database</span></span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="ex">download-ensembl-variations</span> <span class="at">-v</span> 1 <span class="at">-available_species</span> <span class="at">-o</span> species_with_variations_ensembl.tsv</span>
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a></span>
<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="co">## Check the content of the result file</span></span>
<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a><span class="fu">more</span> species_with_variations_ensembl.tsv</span>
<span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a></span>
<span id="cb5-7"><a href="#cb5-7" tabindex="-1"></a><span class="co">## Count genomes with variations available at Ensembl</span></span>
<span id="cb5-8"><a href="#cb5-8" tabindex="-1"></a><span class="fu">grep</span> <span class="at">-v</span> <span class="st">'^;'</span> species_with_variations_ensembl.tsv <span class="kw">|</span> <span class="fu">wc</span> <span class="at">-l</span></span>
<span id="cb5-9"><a href="#cb5-9" tabindex="-1"></a><span class="co">## Result : 23 on August 6, 2018</span></span></code></pre></div>
<p>Note: as an alternative to <code>download-ensembl-variations</code>,
we could have used the command <code>ìnstall-ensembl-genomes</code> with
the option <code>-task variations</code>.</p>
<p>We can now download all the variations available for the yeast.</p>
<div class="sourceCode" id="cb6"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="co">## Download all variations for a selected organism on your server</span></span>
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="ex">download-ensembl-variations</span> <span class="at">-v</span> 1 <span class="at">-species</span> Saccharomyces_cerevisiae</span></code></pre></div>
<p>Variation files are stored in a specific subfolder for the specified
organism.</p>
<div class="sourceCode" id="cb7"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co">## Check the content of the variation directory for the yeast</span></span>
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/variation-scan_demo.mk <span class="dt">\</span></span>
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a> SPECIES=Saccharomyces_cerevisiae ASSEMBLY=R64-1-1 <span class="dt">\</span></span>
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a> variation_stats</span></code></pre></div>
<p>This command will indicate the location of the variation directory on
your server, and count the number of lines for each variation file
(there is one separate file per chromosome or contig).</p>
<hr />
</div>
<div id="installing-the-human-genome-and-human-polymorphic-variations"
class="section level1" number="7">
<h1><span class="header-section-number">7</span> Installing the Human
genome and human polymorphic variations</h1>
<p>In the examples above we intently installed the smallest genome
available at Ensembl, in order to obtain the results in a reasonable
time and with a reasonable disk space occupancy.</p>
<p>The installation of Metazoa occupies much more space, and takes a
significantly longer time.</p>
<p>We summarize hereafter the commands to download and install the Human
genome, its annotations, and the variations from Ensembl. To this
purpose, we customize the options of
<code>install-ensembl-genomes</code> in order to :</p>
<ul>
<li>download the genome sequence,</li>
<li>download genome annotations (features),</li>
<li>download variations,</li>
<li>update RSAT configuration in order to enable the downloaded
genome,</li>
<li>install the genome on RSAT (compute oligo and dyad frequencies +
some other tasks)</li>
</ul>
<p><strong>Beware:</strong> the following command will mobilize ~11.7 Gb
of disk space for the genome + 11.5 Gb for the variations.</p>
<div class="sourceCode" id="cb8"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a></span>
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a><span class="co">## Install Human genome from Ensembl, including polymorphic variations</span></span>
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a><span class="ex">install-ensembl-genome</span> <span class="at">-v</span> 2 <span class="at">-db</span> ensembl <span class="at">-org</span> Homo_sapiens <span class="at">-task</span> genome,features,config,install,variations</span>
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a></span>
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a><span class="co">## Check the disk space occupied by the different folders</span></span>
<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="fu">du</span> <span class="at">-sm</span> data/genomes/Homo_sapiens_GRCh38/<span class="pp">*</span></span>
<span id="cb8-7"><a href="#cb8-7" tabindex="-1"></a></span>
<span id="cb8-8"><a href="#cb8-8" tabindex="-1"></a><span class="co">## Result (2018-08-06) in Megabytes per folder</span></span>
<span id="cb8-9"><a href="#cb8-9" tabindex="-1"></a><span class="co"># 11701 data/genomes/Homo_sapiens_GRCh38/genome</span></span>
<span id="cb8-10"><a href="#cb8-10" tabindex="-1"></a><span class="co"># 18 data/genomes/Homo_sapiens_GRCh38/oligo-frequencies</span></span>
<span id="cb8-11"><a href="#cb8-11" tabindex="-1"></a><span class="co"># 11544 data/genomes/Homo_sapiens_GRCh38/variations</span></span></code></pre></div>
</div>
<div id="installing-a-genome-from-ensembl-genomes"
class="section level1" number="8">
<h1><span class="header-section-number">8</span> Installing a genome
from Ensembl Genomes</h1>
<p>For all non Vertebrate organisms (Protists, Fungi, Plants, Bacteria,
Metazoa) please check <a
href="https://rsa-tools.github.io/managing-RSAT/genome_installation/install_organisms_ensembl_genomes.html">Installing
genomes from Ensembl Genomes</a>.</p>
</div>
</div>
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