-
Notifications
You must be signed in to change notification settings - Fork 1
/
octopus_genome.html
307 lines (295 loc) · 12.3 KB
/
octopus_genome.html
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
<!DOCTYPE HTML>
<!--
Landed by HTML5 UP
html5up.net | @ajlkn
Free for personal and commercial use under the CCA 3.0 license (html5up.net/license)
-->
<html>
<head>
<title>
Octopus chierchiae genome assembly
</title>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no" />
<link rel="stylesheet" href="assets/css/jquery-ui.min.css" />
<link rel="stylesheet" href="assets/css/jquery-ui.structure.min.css" />
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css" integrity="sha384-JcKb8q3iqJ61gNV9KGb8thSsNjpSL0n8PARn9HuZOnIxN0hoP+VmmDGMN5t9UJ0Z" crossorigin="anonymous" />
<noscript><link rel="stylesheet" href="assets/css/noscript.css" /></noscript>
<link rel="stylesheet" href="assets/css/main.css" />
<link rel="stylesheet" href="assets/css/loyal_mods.css" />
</head>
<body class="is-preload">
<div id="page-wrapper">
<!-- Header -->
<header id="header">
<h1 id="logo">
<a href="index.html"> <img id="shield" src="images/medicine.shield.small.white.png" height="40" alt=""/>Goff Lab</a>
</h1>
<nav id="nav">
<ul>
<li><a href="index.html">Home</a></li>
<!-- <li><a href="news.html">News</a></li> -->
<li><a href="people.html">People</a></li>
<li><a href="#">Research</a>
<ul>
<li><a href="preprints.html">Preprints</a></li>
<li><a href="publications.html">Publications</a></li>
<li><a href="software.html">Software</a></li>
<li><a href="datasets.html">Datasets</a></li>
</ul>
</li>
<!-- <li><a href="teaching.html">Teaching</a></li> -->
<!--
<li><a href="#">Resources</a>
<ul>
<li><a href="members.html">Lab Members</a></li>
<li><a href="links.html">Links</a></li>
</ul>
</li>
-->
<!-- <li><a href="blog.html">Blog</a></li> -->
<li><a href="lab_resources.html">Resources</a></li>
<li><a href="join.html">Opportunites</a></li>
<li><a href="contact.html">Contact Us</a></li>
<!--<li><a href="#" class="button primary">Sign Up</a></li>-->
</ul>
</nav>
</header>
<!-- Main -->
<div id="main" class="wrapper style1">
<div class="container">
<header class="major">
<h2>Octopus chierchiae genome assembly</h2>
</header>
<!-- Content -->
<section id="content">
<div class="box alt">
<img src="images/ochier_genome/Och1.jpeg" alt="Octopus chierchiae" class="image left">
<img src="images/ochier_genome/Och2.jpeg" alt="Octopus chierchiae" class="image left">
<img src="images/ochier_genome/Och3.jpeg" alt="Octopus chierchiae" class="image left">
</div>
<h3>Workflow</h3>
<img src="images/ochier_genome/ochier_assembly_workflow_20230208.png" alt="Workflow diagram" class="rounded mx-auto d-block center" style="width:50%;height:50%;">
<h3>Downloads</h3>
<h4>GENOME</h4>
<table>
<tr>
<th>File</th>
<th>URL</th>
<th>Type</th>
<th>Size</th>
<th>MD5</th>
</tr>
<tr>
<td>Haplotype-resolved Assembled Genome (chromosomes only, hap1)</td>
<td><a href="https://dl.dropboxusercontent.com/s/b5xhmdji66tmm9g/Ochierchiae_hap1_scaffold_v1.0_20230204_scaffolds_final_chrom.fa.gz" target="_blank">Ochierchiae_hap1_scaffold_v1.0_20230204_scaffolds_final_chrom.fa.gz</a></td>
<td>Gzipped FASTA</td>
<td>1.3 GB</td>
<td>91bf2620fa15267a2ee6154c475f6978</td>
</tr>
<tr>
<td>Unscaffolded contigs (hap1)</td>
<td><a href="https://dl.dropboxusercontent.com/s/qyhhielqzijklb1/Ochierchiae_hap1_scaffold_v1.0_20230204_scaffolds_final_scaffolds.fa.gz" target="_blank">Ochierchiae_hap1_scaffold_v1.0_20230204_scaffolds_final_scaffolds.fa.gz</a></td>
<td>Gzipped FASTA</td>
<td>39 MB</td>
<td>e4d69881d05137ed2848342fc44393f4</td>
</tr>
<tr>
<td>Repeatmasker-masked assembly (primary chromosomes only)</td>
<td><a href="https://dl.dropboxusercontent.com/s/9ix5svkfeuqb3ch/Ochierchiae_hap1_scaffold_v1.0_20230204_scaffolds_final_chrom_masked.fa.gz" target="_blank">Ochierchiae_hap1_scaffold_v1.0_20230204_scaffolds_final_chrom_masked.fa.gz</a></td>
<td>Gzipped FASTA</td>
<td>410 MB</td>
<td>948832d9d2dd2ff20649ce47ef792122</td>
</tr>
<tr>
<td>Hi-C contact matrix</td>
<td><a href="https://dl.dropboxusercontent.com/s/y8fb90ctbxc24k3/hap1_contact_map.hic" target="_blank">hap1_contact_map.hic</a></td>
<td>HIC</td>
<td>2.5 GB</td>
<td>444dc4579cb209ebebd68a6b32c9d9d9</td>
</tr>
<tr>
<td>RepeatModeler 2.0 output (learned from O.chierchiae hap1 scaffolded assembly)</td>
<td><a href="https://dl.dropboxusercontent.com/s/gmb6fby0g181phl/ochierchiae-families.fa" target="_blank">ochierchiae-families.fa</a></td>
<td>Fasta</td>
<td>3.0 MB</td>
<td>a9f4d3718bb2d914dd5c649f9711750d</td>
</tr>
<tr>
<td>Repeat Annotation (against O.chierchiae hap1 scaffolded assembly)</td>
<td><a href="https://dl.dropboxusercontent.com/s/12la16tmbs1yayi/Ochierchiae_hap1_scaffold_v1.0_20230221_repeatmasker_features.bed.gz" target="_blank">Ochierchiae_hap1_scaffold_v1.0_20230221_repeatmasker_features.bed.gz</a></td>
<td>Gzipped BED</td>
<td>663.3 MB</td>
<td>3b2e2064a2ed45e1e8076dcab164664f</td>
</tr>
</table>
<h4>TRANSCRIPTOME</h4>
<table>
<tr>
<th>File</th>
<th>url</th>
<th>Type</th>
<th>Size</th>
<th>MD5</th>
</tr>
<tr>
<td>Assembled reference transcriptome (stringtie, unannotated)</td>
<td><a href="https://dl.dropboxusercontent.com/s/ajscr4jzb1kkn6o/Ochier_stringtie_merged_assembly_20230207.gtf" target="_blank">Ochier_stringtie_merged_assembly_20230207.gtf</a></td>
<td>GTF</td>
<td>52 MB</td>
<td>9db68ca97be46682d12619760d747c75</td>
</tr>
<tr>
<td>Assembled reference transcriptome sequences (stringtie)</td>
<td><a href="https://dl.dropboxusercontent.com/s/qzdtbpjxz1mzc4e/Ochier_stringtie_merged_assembly_20230207.fa.gz" target="_blank">Ochier_stringtie_merged_assembly_20230207.fa.gz</a></td>
<td>Gzipped FASTA</td>
<td>32 MB</td>
<td>66524aeca6a845ebee08be0d4f162dd2</td>
</tr>
<tr>
<td>Assembled reference transcriptome sequence annotations (stringtie)</td>
<td><a href="https://www.dropbox.com/scl/fi/jrud32fspmlolxtsyph6f/stringtie_merged_assembly_annotation_20230505.xlsx?dl=0&rlkey=go2cfi00ws6lg7b3hn5wafr96" target="_blank">stringtie_merged_assembly_annotation_20230505.xlsx</a></td>
<td>Gzipped FASTA</td>
<td>32 MB</td>
<td>66524aeca6a845ebee08be0d4f162dd2</td>
</tr>
<tr>
<td>O.bimaculoides transcriptome liftoff</td>
<td><a href="https://dl.dropboxusercontent.com/s/a4cb0buuz01bvag/Ochier_liftoff_from_Obimac_20230207.gff3" target="_blank">Ochier_liftoff_from_Obimac_20230207.gff3</a></td>
<td>GFF3</td>
<td>25 MB</td>
<td>255427d6f9e72fb3b3529961c24614df</td>
</tr>
<tr>
<td><em>de novo</em> Transcriptome assembly sequence (Trinity, unannotated)</td>
<td><a href="https://dl.dropboxusercontent.com/s/yg9qa2ljf159ha9/Ochierchiae.Trinity.fa.gz" target="_blank">Ochierchiae.Trinity.fa.gz</a></td>
<td>Gzipped FASTA</td>
<td>96 MB</td>
<td>b6022ca6e1f5464be6137a8fc86d858e</td>
</tr>
<tr>
<td><em>de novo</em> Transcriptome assembly alignment to reference genome (Trinity, unannotated)</td>
<td><a href="https://dl.dropboxusercontent.com/s/r9kmsp5x64jfaij/Trinity_aln_to_ref_hap1.gff3.gz" target="_blank">Trinity_aln_to_ref_hap1.gff3.gz</a></td>
<td>Gzipped GFF3</td>
<td>83 MB</td>
<td>dd5b3ab0c43953160656a9015bea9c72</td>
</tr>
</table>
<h3>Stats</h3>
<img src="images/ochier_genome/nxplot.png" alt="N(x) plot" class="image left">
<img src="images/ochier_genome/cum_assembly.png" alt="Cumulative Assembly Length" class="image left">
<table>
<tr>
<th>Param</th>
<th>Value</th>
</tr>
<tr>
<td>Genome size</td>
<td> 5,180,130,439 bases</td>
</tr>
<tr>
<td>Total Number of chromosome scaffolds</td>
<td>30</td>
</tr>
<tr>
<td>Total Number of contigs</td>
<td>5,569</td>
</tr>
<tr>
<td>Largest scaffold</td>
<td>413,096,176 bases</td>
</tr>
<tr>
<td>GC content</td>
<td> 35.87%</td>
</tr>
<tr>
<td>N50</td>
<td>218,401,579 bases</td>
</tr>
<tr>
<td>L50</td>
<td>9</td>
</tr>
<tr>
<td>N90</td>
<td>76,540,371 bases</td>
</tr>
<tr>
<td>L90</td>
<td>25</td>
</tr>
<tr>
<td>% of bases in chromosomes</td>
<td>96.09%</td>
</tr>
<tr>
<td>Total length of scaffolded chromosomes</td>
<td>4,977,408,424 bases</td>
</tr>
<tr>
<td>Number of gaps</td>
<td> 5,061 </td>
</tr>
<tr>
<td>BUSCO metazoa_odb10</td>
<td>C:94.4%[S:93.6%,D:0.8%],F:3.5%,M:2.1%,n:954</td>
</tr>
<tr>
<td>Number of genes</td>
<td>TBD</td>
</tr>
</table>
</section>
</div>
</div>
</div>
<!-- Footer -->
<footer id="footer">
<ul class="icons">
<li><a href="https://twitter.com/intent/tweet?original_referer=https%3A%2F%2Fwww.sharelinkgenerator.com%2F&ref_src=twsrc%5Etfw&text=Share%20Link%20Generator%3A%20Facebook%2C%20Twitter%2C%20LinkedIn%2C%20Pinterest%2C%20and%20Email%20mailto%20forms&tw_p=tweetbutton&url=https%3A%2F%2Fwww.sharelinkgenerator.com%2F&via=twitterapi" class="icon brands alt fa-twitter"><span class="label">Twitter</span></a></li>
<!-- <li><a href="#" class="icon brands alt fa-facebook-f"><span class="label">Facebook</span></a></li> -->
<!-- <li><a href="#" class="icon brands alt fa-linkedin-in"><span class="label">LinkedIn</span></a></li> -->
<!-- <li><a href="#" class="icon brands alt fa-instagram"><span class="label">Instagram</span></a></li> -->
<li><a href="http://github.com/gofflab/" class="icon brands alt fa-github"><span class="label">GitHub</span></a></li>
<li><a href="mailto:loyalgoff@jhmi.edu" class="icon solid alt fa-envelope"><span class="label">Email</span></a></li>
</ul>
<ul class="copyright">
<li>© Goff Lab - JHU. All rights reserved.</li><li>Design: <a href="http://html5up.net">HTML5 UP</a></li>
</ul>
</footer>
<!-- Scripts -->
<script src="assets/js/jquery.min.js"></script>
<script src="assets/js/jquery.scrolly.min.js"></script>
<script src="assets/js/jquery.dropotron.min.js"></script>
<script src="assets/js/jquery.scrollex.min.js"></script>
<script src="assets/js/browser.min.js"></script>
<script src="assets/js/breakpoints.min.js"></script>
<script src="assets/js/util.js"></script>
<script src="assets/js/main.js"></script>
<script src="assets/js/jquery-ui.min.js"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js" integrity="sha384-B4gt1jrGC7Jh4AgTPSdUtOBvfO8shuf57BaghqFfPlYxofvL8/KUEfYiJOMMV+rV" crossorigin="anonymous"></script>
<script type='text/javascript' src='https://d1bxh8uas1mnw7.cloudfront.net/assets/embed.js'></script>
<script>
$( function() {
$( "#accordion" ).accordion();
} );
</script>
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','http://www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-318359-8', 'auto');
ga('send', 'pageview');
</script>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-X36CPG7L73"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-X36CPG7L73');
</script>
</body>
</html>