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diff --git a/doc/web/download.html b/doc/web/download.html new file mode 100644 index 0000000..879e8d4 --- /dev/null +++ b/doc/web/download.html @@ -0,0 +1,375 @@ +<?xml version="1.0" encoding="utf-8"?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" +"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 --> +<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> +<meta name="viewport" content="width=device-width, initial-scale=1" /> +<title>Download</title> +<meta name="generator" content="Org mode" /> +<meta name="author" content="Pjotr Prins" /> +<style type="text/css"> + <!--/*--><![CDATA[/*><!--*/ + .title { text-align: center; + margin-bottom: .2em; } + .subtitle { text-align: center; + font-size: medium; + font-weight: bold; + margin-top:0; } + .todo { font-family: monospace; color: red; } + .done { font-family: monospace; color: green; } + .priority { font-family: monospace; color: orange; } + .tag { background-color: #eee; font-family: monospace; + padding: 2px; font-size: 80%; font-weight: normal; } + .timestamp { color: #bebebe; } + .timestamp-kwd { color: #5f9ea0; } + .org-right { margin-left: auto; margin-right: 0px; text-align: right; } + .org-left { margin-left: 0px; margin-right: auto; text-align: left; } + .org-center { margin-left: auto; margin-right: auto; text-align: center; } + .underline { text-decoration: underline; } + #postamble p, #preamble p { font-size: 90%; margin: .2em; } + p.verse { margin-left: 3%; } + pre { + border: 1px solid #ccc; + box-shadow: 3px 3px 3px #eee; + padding: 8pt; + font-family: monospace; + overflow: auto; + margin: 1.2em; + } + pre.src { + position: relative; + overflow: visible; + padding-top: 1.2em; + } + pre.src:before { + display: none; + position: absolute; + background-color: white; + top: -10px; + right: 10px; + padding: 3px; + border: 1px solid black; + } + pre.src:hover:before { display: inline;} + /* Languages per Org manual */ + pre.src-asymptote:before { content: 'Asymptote'; } + pre.src-awk:before { content: 'Awk'; } + pre.src-C:before { content: 'C'; } + /* pre.src-C++ doesn't work in CSS */ + pre.src-clojure:before { content: 'Clojure'; } + pre.src-css:before { content: 'CSS'; } + pre.src-D:before { content: 'D'; } + pre.src-ditaa:before { content: 'ditaa'; } + pre.src-dot:before { content: 'Graphviz'; } + pre.src-calc:before { content: 'Emacs Calc'; } + pre.src-emacs-lisp:before { content: 'Emacs Lisp'; } + pre.src-fortran:before { content: 'Fortran'; } + pre.src-gnuplot:before { content: 'gnuplot'; } + pre.src-haskell:before { content: 'Haskell'; } + pre.src-hledger:before { content: 'hledger'; } + pre.src-java:before { content: 'Java'; } + pre.src-js:before { content: 'Javascript'; } + pre.src-latex:before { content: 'LaTeX'; } + pre.src-ledger:before { content: 'Ledger'; } + pre.src-lisp:before { content: 'Lisp'; } + pre.src-lilypond:before { content: 'Lilypond'; } + pre.src-lua:before { content: 'Lua'; } + pre.src-matlab:before { content: 'MATLAB'; } + pre.src-mscgen:before { content: 'Mscgen'; } + pre.src-ocaml:before { content: 'Objective Caml'; } + pre.src-octave:before { content: 'Octave'; } + pre.src-org:before { content: 'Org mode'; } + pre.src-oz:before { content: 'OZ'; } + pre.src-plantuml:before { content: 'Plantuml'; } + pre.src-processing:before { content: 'Processing.js'; } + pre.src-python:before { content: 'Python'; } + pre.src-R:before { content: 'R'; } + pre.src-ruby:before { content: 'Ruby'; } + pre.src-sass:before { content: 'Sass'; } + pre.src-scheme:before { content: 'Scheme'; } + pre.src-screen:before { content: 'Gnu Screen'; } + pre.src-sed:before { content: 'Sed'; } + pre.src-sh:before { content: 'shell'; } + pre.src-sql:before { content: 'SQL'; } + pre.src-sqlite:before { content: 'SQLite'; } + /* additional languages in org.el's org-babel-load-languages alist */ + pre.src-forth:before { content: 'Forth'; } + pre.src-io:before { content: 'IO'; } + pre.src-J:before { content: 'J'; } + pre.src-makefile:before { content: 'Makefile'; } + pre.src-maxima:before { content: 'Maxima'; } + pre.src-perl:before { content: 'Perl'; } + pre.src-picolisp:before { content: 'Pico Lisp'; } + pre.src-scala:before { content: 'Scala'; } + pre.src-shell:before { content: 'Shell Script'; } + pre.src-ebnf2ps:before { content: 'ebfn2ps'; } + /* additional language identifiers per "defun org-babel-execute" + in ob-*.el */ + pre.src-cpp:before { content: 'C++'; } + pre.src-abc:before { content: 'ABC'; } + pre.src-coq:before { content: 'Coq'; } + pre.src-groovy:before { content: 'Groovy'; } + /* additional language identifiers from org-babel-shell-names in + ob-shell.el: ob-shell is the only babel language using a lambda to put + the execution function name together. */ + pre.src-bash:before { content: 'bash'; } + pre.src-csh:before { content: 'csh'; } + pre.src-ash:before { content: 'ash'; } + pre.src-dash:before { content: 'dash'; } + pre.src-ksh:before { content: 'ksh'; } + pre.src-mksh:before { content: 'mksh'; } + pre.src-posh:before { content: 'posh'; } + /* Additional Emacs modes also supported by the LaTeX listings package */ + pre.src-ada:before { content: 'Ada'; } + pre.src-asm:before { content: 'Assembler'; } + pre.src-caml:before { content: 'Caml'; } + pre.src-delphi:before { content: 'Delphi'; } + pre.src-html:before { content: 'HTML'; } + pre.src-idl:before { content: 'IDL'; } + pre.src-mercury:before { content: 'Mercury'; } + pre.src-metapost:before { content: 'MetaPost'; } + pre.src-modula-2:before { content: 'Modula-2'; } + pre.src-pascal:before { content: 'Pascal'; } + pre.src-ps:before { content: 'PostScript'; } + pre.src-prolog:before { content: 'Prolog'; } + pre.src-simula:before { content: 'Simula'; } + pre.src-tcl:before { content: 'tcl'; } + pre.src-tex:before { content: 'TeX'; } + pre.src-plain-tex:before { content: 'Plain TeX'; } + pre.src-verilog:before { content: 'Verilog'; } + pre.src-vhdl:before { content: 'VHDL'; } + pre.src-xml:before { content: 'XML'; } + pre.src-nxml:before { content: 'XML'; } + /* add a generic configuration mode; LaTeX export needs an additional + (add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */ + pre.src-conf:before { content: 'Configuration File'; } + + table { border-collapse:collapse; } + caption.t-above { caption-side: top; } + caption.t-bottom { caption-side: bottom; } + td, th { vertical-align:top; } + th.org-right { text-align: center; } + th.org-left { text-align: center; } + th.org-center { text-align: center; } + td.org-right { text-align: right; } + td.org-left { text-align: left; } + td.org-center { text-align: center; } + dt { font-weight: bold; } + .footpara { display: inline; } + .footdef { margin-bottom: 1em; } + .figure { padding: 1em; } + .figure p { text-align: center; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } + .inlinetask { + padding: 10px; + border: 2px solid gray; + margin: 10px; + background: #ffffcc; + } + #org-div-home-and-up + { text-align: right; font-size: 70%; white-space: nowrap; } + textarea { overflow-x: auto; } + .linenr { font-size: smaller } + .code-highlighted { background-color: #ffff00; } + .org-info-js_info-navigation { border-style: none; } + #org-info-js_console-label + { font-size: 10px; font-weight: bold; white-space: nowrap; } + .org-info-js_search-highlight + { background-color: #ffff00; color: #000000; font-weight: bold; } + .org-svg { width: 90%; } + /*]]>*/--> +</style> +<script type="text/javascript"> +/* +@licstart The following is the entire license notice for the +JavaScript code in this tag. + +Copyright (C) 2012-2020 Free Software Foundation, Inc. + +The JavaScript code in this tag is free software: you can +redistribute it and/or modify it under the terms of the GNU +General Public License (GNU GPL) as published by the Free Software +Foundation, either version 3 of the License, or (at your option) +any later version. The code is distributed WITHOUT ANY WARRANTY; +without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU GPL for more details. + +As additional permission under GNU GPL version 3 section 7, you +may distribute non-source (e.g., minimized or compacted) forms of +that code without the copy of the GNU GPL normally required by +section 4, provided you include this license notice and a URL +through which recipients can access the Corresponding Source. + + +@licend The above is the entire license notice +for the JavaScript code in this tag. +*/ +<!--/*--><![CDATA[/*><!--*/ + function CodeHighlightOn(elem, id) + { + var target = document.getElementById(id); + if(null != target) { + elem.cacheClassElem = elem.className; + elem.cacheClassTarget = target.className; + target.className = "code-highlighted"; + elem.className = "code-highlighted"; + } + } + function CodeHighlightOff(elem, id) + { + var target = document.getElementById(id); + if(elem.cacheClassElem) + elem.className = elem.cacheClassElem; + if(elem.cacheClassTarget) + target.className = elem.cacheClassTarget; + } +/*]]>*///--> +</script> +</head> +<body> +<div id="content"> +<h1 class="title">Download</h1> +<div id="table-of-contents"> +<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> +<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> +</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 class="outline-text-2" id="text-1"> +<p> +The <b>public sequence resource</b> provides all uploaded sequences as +FASTA files. They can be referred to from metadata individually. We +also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup.fasta">FASTA download</a>. +</p> +</div> +</div> + +<div id="outline-container-orgc0ce14b" class="outline-2"> +<h2 id="orgc0ce14b"><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 +can be loaded into any RDF triple-store. We provide a Virtuoso SPARQL +endpoint ourselves which can be queried from +<a href="http://sparql.genenetwork.org/sparql/">http://sparql.genenetwork.org/sparql/</a>. Query examples can be found in +our <a href="https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/using-covid-19-pubseq-part1.org">BLOG</a>. +</p> + +<p> +The Swiss Institute of Bioinformatics has included this data in +<a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> and made it part of <a href="https://www.uniprot.org/">Uniprot</a>. +</p> + +<p> +An RDF file that includes the sequences themselves in a variation +graph can be downloaded from below Pangenome RDF format. +</p> +</div> +</div> + +<div id="outline-container-org52c7997" class="outline-2"> +<h2 id="org52c7997"><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 +(VG) provide a succinct encoding of the sequences of many genomes. +</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 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 +by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. +</p> +</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 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 +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 class="outline-text-3" id="text-3-3"> +<p> +An RDF file that includes the sequences themselves in a variation +graph can be downloaded from +<a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">relabeledSeqs-dedup-relabeledSeqs-dedup.ttl.xz</a>. +</p> +</div> +</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 class="outline-text-3" id="text-3-4"> +<p> +The many JSON files that are named as +<a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">results/1/chunk001200.bin1.schematic.json</a> are consumed by the +Pangenome browser. +</p> +</div> +</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 class="outline-text-2" id="text-4"> +<p> +Including in below link is a log file of the last workflow runs. +</p> +</div> +</div> + +<div id="outline-container-orga53b821" class="outline-2"> +<h2 id="orga53b821"><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> +<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>. +</div> +</body> +</html> |