blob: 879e8d4340dff3e248c6646a6d784751fc61042f (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
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>
|
