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| author | Pjotr Prins | 2020-05-24 11:33:07 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2020-05-24 11:33:07 -0500 |
| commit | e5be5fe049bb0319fedb65248cb562369735d879 (patch) | |
| tree | cfb068cea2cabdb091b340b507edb38b855f6317 /doc/web/download.html | |
| parent | 17c698f29742cbd24bdbf79e613a0124fce20316 (diff) | |
| download | bh20-seq-resource-e5be5fe049bb0319fedb65248cb562369735d879.tar.gz bh20-seq-resource-e5be5fe049bb0319fedb65248cb562369735d879.tar.lz bh20-seq-resource-e5be5fe049bb0319fedb65248cb562369735d879.zip | |
Colors and protein prediction
Diffstat (limited to 'doc/web/download.html')
| -rw-r--r-- | doc/web/download.html | 113 |
1 files changed, 83 insertions, 30 deletions
diff --git a/doc/web/download.html b/doc/web/download.html index 879e8d4..493af11 100644 --- a/doc/web/download.html +++ b/doc/web/download.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-05-24 Sun 11:11 --> +<!-- 2020-05-24 Sun 11:29 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>Download</title> @@ -247,24 +247,32 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#orge184013">1. FASTA files</a></li> -<li><a href="#orgc0ce14b">2. Metadata</a></li> -<li><a href="#org52c7997">3. Pangenome</a> +<li><a href="#org42addaa">1. FASTA files</a></li> +<li><a href="#org04bd8c7">2. Metadata</a></li> +<li><a href="#orgead2f03">3. Pangenome</a> <ul> -<li><a href="#orgba61745">3.1. Pangenome GFA format</a></li> -<li><a href="#org6474dfc">3.2. Pangenome in ODGI format</a></li> -<li><a href="#orge3a3726">3.3. Pangenome RDF format</a></li> -<li><a href="#org359cc22">3.4. Pangenome Browser format</a></li> +<li><a href="#org8ea7d40">3.1. Pangenome GFA format</a></li> +<li><a href="#orge7808d6">3.2. Pangenome in ODGI format</a></li> +<li><a href="#orgaadcde8">3.3. Pangenome RDF format</a></li> +<li><a href="#orga3a0408">3.4. Pangenome Browser format</a></li> +</ul> +</li> +<li><a href="#org1bbb7e6">4. Log of workflow output</a></li> +<li><a href="#orgd16b2c8">5. All files</a></li> +<li><a href="#org9d40ed2">6. Planned</a> +<ul> +<li><a href="#org70cb9d5">6.1. Raw sequence data</a></li> +<li><a href="#org38cfa2e">6.2. Multiple Sequence Alignment (MSA)</a></li> +<li><a href="#org507c7dd">6.3. Phylogenetic tree</a></li> +<li><a href="#orgca26edf">6.4. Protein prediction</a></li> </ul> </li> -<li><a href="#org488e901">4. Log of workflow output</a></li> -<li><a href="#orga53b821">5. All files</a></li> </ul> </div> </div> -<div id="outline-container-orge184013" class="outline-2"> -<h2 id="orge184013"><span class="section-number-2">1</span> FASTA files</h2> +<div id="outline-container-org42addaa" class="outline-2"> +<h2 id="org42addaa"><span class="section-number-2">1</span> FASTA files</h2> <div class="outline-text-2" id="text-1"> <p> The <b>public sequence resource</b> provides all uploaded sequences as @@ -274,8 +282,8 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l </div> </div> -<div id="outline-container-orgc0ce14b" class="outline-2"> -<h2 id="orgc0ce14b"><span class="section-number-2">2</span> Metadata</h2> +<div id="outline-container-org04bd8c7" class="outline-2"> +<h2 id="org04bd8c7"><span class="section-number-2">2</span> Metadata</h2> <div class="outline-text-2" id="text-2"> <p> Metadata can be downloaded as <a href="https://www.w3.org/TR/turtle/">Turtle RDF</a> as a <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">mergedmetadat.ttl</a> which @@ -297,8 +305,8 @@ graph can be downloaded from below Pangenome RDF format. </div> </div> -<div id="outline-container-org52c7997" class="outline-2"> -<h2 id="org52c7997"><span class="section-number-2">3</span> Pangenome</h2> +<div id="outline-container-orgead2f03" class="outline-2"> +<h2 id="orgead2f03"><span class="section-number-2">3</span> Pangenome</h2> <div class="outline-text-2" id="text-3"> <p> Pangenome data is made available in multiple guises. Variation graphs @@ -306,8 +314,8 @@ Pangenome data is made available in multiple guises. Variation graphs </p> </div> -<div id="outline-container-orgba61745" class="outline-3"> -<h3 id="orgba61745"><span class="section-number-3">3.1</span> Pangenome GFA format</h3> +<div id="outline-container-org8ea7d40" class="outline-3"> +<h3 id="org8ea7d40"><span class="section-number-3">3.1</span> Pangenome GFA format</h3> <div class="outline-text-3" id="text-3-1"> <p> <a href="https://github.com/GFA-spec/GFA-spec">GFA</a> is a standard for graphical fragment assembly and consumed @@ -316,18 +324,18 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. </div> </div> -<div id="outline-container-org6474dfc" class="outline-3"> -<h3 id="org6474dfc"><span class="section-number-3">3.2</span> Pangenome in ODGI format</h3> +<div id="outline-container-orge7808d6" class="outline-3"> +<h3 id="orge7808d6"><span class="section-number-3">3.2</span> Pangenome in ODGI format</h3> <div class="outline-text-3" id="text-3-2"> <p> -<a href="https://github.com/vgteam/odgi">ODGI</a> is a format that supports an optimized dynamic genome/graph +<a href="https://github.com/vgteam/odgi">ODGI</a> is a format that supports an optimised dynamic genome/graph implementation. </p> </div> </div> -<div id="outline-container-orge3a3726" class="outline-3"> -<h3 id="orge3a3726"><span class="section-number-3">3.3</span> Pangenome RDF format</h3> +<div id="outline-container-orgaadcde8" class="outline-3"> +<h3 id="orgaadcde8"><span class="section-number-3">3.3</span> Pangenome RDF format</h3> <div class="outline-text-3" id="text-3-3"> <p> An RDF file that includes the sequences themselves in a variation @@ -338,8 +346,8 @@ graph can be downloaded from </div> -<div id="outline-container-org359cc22" class="outline-3"> -<h3 id="org359cc22"><span class="section-number-3">3.4</span> Pangenome Browser format</h3> +<div id="outline-container-orga3a0408" class="outline-3"> +<h3 id="orga3a0408"><span class="section-number-3">3.4</span> Pangenome Browser format</h3> <div class="outline-text-3" id="text-3-4"> <p> The many JSON files that are named as @@ -350,8 +358,8 @@ Pangenome browser. </div> </div> -<div id="outline-container-org488e901" class="outline-2"> -<h2 id="org488e901"><span class="section-number-2">4</span> Log of workflow output</h2> +<div id="outline-container-org1bbb7e6" class="outline-2"> +<h2 id="org1bbb7e6"><span class="section-number-2">4</span> Log of workflow output</h2> <div class="outline-text-2" id="text-4"> <p> Including in below link is a log file of the last workflow runs. @@ -359,17 +367,62 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-orga53b821" class="outline-2"> -<h2 id="orga53b821"><span class="section-number-2">5</span> All files</h2> +<div id="outline-container-orgd16b2c8" class="outline-2"> +<h2 id="orgd16b2c8"><span class="section-number-2">5</span> All files</h2> <div class="outline-text-2" id="text-5"> <p> <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/</a> </p> </div> </div> + +<div id="outline-container-org9d40ed2" class="outline-2"> +<h2 id="org9d40ed2"><span class="section-number-2">6</span> Planned</h2> +<div class="outline-text-2" id="text-6"> +<p> +We are planning the add the following output (see also +</p> +</div> + +<div id="outline-container-org70cb9d5" class="outline-3"> +<h3 id="org70cb9d5"><span class="section-number-3">6.1</span> Raw sequence data</h3> +<div class="outline-text-3" id="text-6-1"> +<p> +See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq tracker</a> and <a href="https://github.com/arvados/bh20-seq-resource/issues/63">BAM tracker</a>. +</p> +</div> +</div> + +<div id="outline-container-org38cfa2e" class="outline-3"> +<h3 id="org38cfa2e"><span class="section-number-3">6.2</span> Multiple Sequence Alignment (MSA)</h3> +<div class="outline-text-3" id="text-6-2"> +<p> +See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker</a>. +</p> +</div> +</div> + +<div id="outline-container-org507c7dd" class="outline-3"> +<h3 id="org507c7dd"><span class="section-number-3">6.3</span> Phylogenetic tree</h3> +<div class="outline-text-3" id="text-6-3"> +<p> +See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo tracker</a>. +</p> +</div> +</div> + +<div id="outline-container-orgca26edf" class="outline-3"> +<h3 id="orgca26edf"><span class="section-number-3">6.4</span> Protein prediction</h3> +<div class="outline-text-3" id="text-6-4"> +<p> +We aim to make protein predictions available. +</p> +</div> +</div> +</div> </div> <div id="postamble" class="status"> -<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-24 Sun 11:11</small>. +<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-24 Sun 11:29</small>. </div> </body> </html> |