tag:blogger.com,1999:blog-71283014314725858272024-03-05T14:01:53.863-08:00UNSW BABS Genome ProjectNews and updates for the BABS Genome education and outreach initiative of the School of Biotechnology and Biomolecular Sciences at UNSW Sydney, Australia. Join us as we sequence, assemble and analyse the genomes of some iconic Australian species.Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-7128301431472585827.post-67766082518170731932018-06-18T04:16:00.004-07:002018-06-26T16:04:44.290-07:00Sequencing snakes: the BABS Genomes at SBRS 2018<p>This month saw the first presentation of the BABS genomes outside UNSW. A poster on the genome assemblies was presented at the <a href="https://www.abacbs.org/sbrs2018">Sydney Bioinformatics Research Symposium 2018</a> (abstract below):
<p><strong>Pseudodiploid pseudo-long-read whole genome sequencing and assembly of <i>Pseudonaja textilis</i> (eastern brown snake) and <i>Notechis scutatus</i> (mainland tiger snake)</strong></p>
<p><u>Richard J Edwards</u>, Timothy G Amos, Joshua Tang, Beni Cawood, Sabrina Rispin, Daniel Enosi Tuipulotu & Paul Waters.</p>
<p>Click on thumbnail for full resolution PDF. If you use anything from this work, please cite: </p>
<blockquote>
<p>Edwards RJ <i>et al.</i> Pseudodiploid pseudo-long-read whole genome sequencing and assembly of <i>Pseudonaja textilis</i> (eastern brown snake) and <i>Notechis scutatus</i> (mainland tiger snake) [version 1; not peer reviewed]. <b><i>F1000Research</i> 2018, 7:753 (poster)</b> (doi: <a href="https://f1000research.com/posters/7-753">10.7490/f1000research.1115550.1</a>)</p>
</blockquote>
<p><a href="https://f1000research.com/posters/7-753" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEpd8LRerJbjHuzctlUCnw9XftThMwA5c-TQItdL3jIlH3_zKwx6akx7gZsT9HG6TQ9IlTa7DjeshjT_J-J5iIue56CJE5Z8o5bWC_SXsaBLj-1B7vkA2lRaV3PLcUWDwCcOP54Nu4NTO0/s800/2018-06-15.SBRS.Edwards.jpg" data-original-width="1132" data-original-height="1600" /></a></p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p>The precipitous drop in sequencing costs over recent years has seen the bottleneck in vertebrate whole genome sequencing (WGS) shift from data generation (sequencing) to data processing (assembly and annotation). Draft genomes generated from cheap shotgun Illumina sequencing tend to be highly fragmented with many tens of thousands of short contigs or scaffolds. This can be improved by preparing multiple paired end and “mate pair” libraries with different insert sizes, but this increases the cost of both sequencing and data storage/analysis. PacBio or Oxford Nanopore long read sequencing enables massive improvements in assembly quality but tends to be prohibitively expensive for organisms with large genome sizes, such as vertebrates. 10x Genomics Chromium “linked read” sequencing offers a solution to this problem. High molecular weight molecules of DNA are barcoded prior to standard shotgun Illumina sequencing. These barcodes can then be used for pseudo-long-read assembly, with improved handling of repetitive regions. Where heterozygous variants are dense enough, haplotypes can be phased to generate a “pseudodiploid” assembly with some regions represented as two alleles. This is all for the cost of an additional library prep with no extra sequencing. But does it work?</p>
<p><a href="http://babsgenome.blogspot.com/">We have sequenced</a> two of the deadliest venomous snakes in Australia using 10x Chromium linked reads: the mainland tiger snake (Notechis scutatus) and the eastern brown snake (Pseudonaja textilis). Supernova v2 assemblies of the data generated exceptionally high quality genomes for the price, with maximum scaffolds over 50 Mb and N50 values of 5.99 Mb for the tiger snake and 14.7 Mb for the brown snake. This was reflected in BUSCO (v2.0.1 short) completeness estimates of 87.3% (tiger snake) and 90.5% (brown snake). These data will be compared to tiger snake WGS using standard paired end Illumina NovaSeq shotgun sequencing, and discussed with respect to some of the downstream opportunities and challenges provided by pseudodiploid genome assemblies. In particular, BUSCO analysis of haploid, pseudodiploid, and non-redundant genome assemblies revealed some interesting and unexpected behaviour of this widely-used tool. We also present results from GenomeR, a Shiny app (in development) for batch kmer genome size estimation (<a href="http://shiny.slimsuite.unsw.edu.au/GenomeR/">http://shiny.slimsuite.unsw.edu.au/GenomeR/</a>).</p>
<p>Snake genomes and ongoing annotation are being made available through the lab Web Apollo browser and search tool (<a href="https://slimsuite.unsw.edu.au/servers/apollo.php">https://slimsuite.unsw.edu.au/servers/apollo.php</a>). We welcome contact from anyone interested in getting involved with the annotation and analysis of these genomes.</p>
</blockquote>
<p>Watch this blog for more details on different aspects of the analysis.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-91079335181003924132017-11-05T19:59:00.000-08:002017-11-05T19:59:31.825-08:00UNSW Genome Annotation workshop, Tuesday 21st November 2017<p>I am pleased to announce that we will be running a replacement for <a href="https://edwardslab.blogspot.com.au/2017/05/unsw-genome-annotation-workshop.html">July’s cancelled Genome Annotation workshop</a> at UNSW on Tuesday 21st November 2017, 1100-1400. This will use WebApollo, which is the genome annotation browser we will be using for community annotation of our snake genomes.</p>
<p>Places are limited but it’s free and you can <a href="https://www.eventbrite.com.au/e/genome-annotation-using-apollo-at-embl-abr-sbi-node-tickets-39312237962">sign up here through Eventbrite</a>.</p>
<h2 id="description">DESCRIPTION</h2>
<p>This workshop will include a short background lecture on the fundamentals of gene prediction and genome annotation followed by a hands-on component where we will conduct manual curation exercises using Apollo.</p>
<p>The workshop has been organised by <a href="https://www.embl-abr.org.au/">EMBL-ABR</a> and will be led by Dr Monica Munoz-Torres from <a href="http://phoenixbioinformatics.org/">Phoenix Bioinformatics</a> who is an expert in genome annotation, <a href="https://www.biocuration.org/about/executive-commitee/">current chair of the International Society for Biocuration Executive Committee</a>, and former Project Manager of the <a href="http://genomearchitect.github.io/">Apollo Project</a>.</p>
<p>Monica will be joining us direct from the San Francisco Bay Area, and we will have locally trained trainers on hand to help and facilitate the workshop locally.</p>
<h2 id="topicstobecovered">TOPICS TO BE COVERED</h2>
<ul>
<li>Genome Annotation - why is it important?</li>
<li>Gene prediction
<ul><li>what is a gene</li>
<li>computation</li>
<li>annotation</li></ul></li>
<li>Genome curation
<ul><li>knowledge</li>
<li>curation - why is this necessary?</li></ul></li>
<li>Structural Annotation using Apollo</li>
<li>Biological principles for curation with Apollo</li>
<li>Apollo functionality: step by step</li>
<li>Curation example</li>
</ul>
<h2 id="requirements">Requirements</h2>
<p>Participants must bring their own eduroam-enabled laptop with either Chrome or Firefox installed.</p>
<h2>Further information</h2>
<p><a href="https://www.embl-abr.org.au/genome-annotation-using-apollo-monica-munoz-torres/">https://www.embl-abr.org.au/genome-annotation-using-apollo-monica-munoz-torres/</a>
or contact Richard Edwards.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-78258640143419302352017-08-28T02:49:00.000-07:002017-10-09T02:56:35.988-07:00Where do our snakes come from?<a href="https://www.venomsupplies.com"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2z5uPdb5kSC9nfvxG00EPtc-liXFx_ZuGJe2WhLKSoBRb6BJK6lsxHqEIfyALlkPlZwQiMHEVQD7f4Cq8IzfbJ1VYFgaLhi7UcbKh61wARbJDm2uNZtXAW-npngbnp6A-Mm0PZER4Z9w/s568/VenomSupplies.png"/></a>
<p>The snakes we are sequencing for the BABS Genome project were kindly supplied by Nathan Dunstan at <a href="http://www.venomsupplies.com">Venom Supplies</a> as a collaborative contribution to Paul Waters and Denis O’Meally when they were at ANU. Thanks Nathan!</p>
<p>We have sequenced two Tiger snake parents, originally caught from the southeast of South Australia (just north of Mt Gambier) in about 2004. They were bred at Venom Supplies, and we have also sequenced one of the babies (sex unknown) born in February 2013.</p>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh44osbxVu0ZDFA3rpCEfJTRDT0b12-ALJ7zBM3BHXXsfDZwjnOHna4XYBf7Mzc5rvz6y6a54rr2mtH62eq1U-n93GC1Y42GbOG6Y7z6T97m6AixmIkhoOqPnY01vcLktWxcMURgJCc6Bg/s1600/Eastern_Tiger_Snake_sq.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh44osbxVu0ZDFA3rpCEfJTRDT0b12-ALJ7zBM3BHXXsfDZwjnOHna4XYBf7Mzc5rvz6y6a54rr2mtH62eq1U-n93GC1Y42GbOG6Y7z6T97m6AixmIkhoOqPnY01vcLktWxcMURgJCc6Bg/s284/Eastern_Tiger_Snake_sq.jpg" data-original-width="1188" data-original-height="1188" align="left" style="margin-right:10px" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiz9ZPJo-SL0wAXJ5AoemoGCAfARJzznAv8FJck0Rmle4qciKDnXm46WWuEY63mPQq89eGNAcMZVyTt8nsFexQRnopysjNGjktSl1TRQ3aWhV8Fch8JqCbqCMKL2JY5IIYOiOaLXAQDBTY/s1600/EBrownSnake-OMeally.jpeg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiz9ZPJo-SL0wAXJ5AoemoGCAfARJzznAv8FJck0Rmle4qciKDnXm46WWuEY63mPQq89eGNAcMZVyTt8nsFexQRnopysjNGjktSl1TRQ3aWhV8Fch8JqCbqCMKL2JY5IIYOiOaLXAQDBTY/s284/EBrownSnake-OMeally.jpeg" data-original-width="427" data-original-height="427"/></a>
<p>The brown snake was a female from a clutch of eggs from a gravid (pregnant) female caught locally in the Barossa.</p>
<h2 id="photocredits">Photo Credits</h2>
<p><a href="https://en.wikipedia.org/wiki/Tiger_snake#/media/File:Eastern_Tiger_Snake.jpg">Tiger Snake</a> (left): Teneche [<a href="http://creativecommons.org/licenses/by-sa/3.0">CC BY-SA 3.0</a>] | Brown Snake (right): Denis O'Meally.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-23255580226769893502017-08-15T04:55:00.001-07:002017-08-15T04:55:33.075-07:00Linked read sequencing is go!<p>We already have <em>over</em> <strong>four billion reads</strong> and <strong>620 GB</strong> of NovaSeq Illumina data for our three tiger snakes; next week’s BABS3291 prac will look at some of the early ABySS assemblies of one of these snakes. </p>
<p>Phase 2 of the sequencing is now go! 10x Chromium linked read libraries were prepared at the Ramaciotti Centre for Genomics last week for one tiger snake and one eastern brown snake. These data promise to make much easier and more intact genome assemblies. We received notification today that the samples have arrived in the KCCG sequencing laboratory at the Garvan Institute for Illumina HiSeq X (“XTen”) sequencing. </p>
<p>Nobody knows how well linked read sequencing, which is optimised for human genomes, will work in a snake but we look forward to finding out!</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-15077764604856777822017-08-04T15:02:00.000-07:002017-08-03T22:05:15.666-07:00Important considerations for sample preparation<p>Today we had a tutorial on the things you need to think about during a genome sequencing project. The first student suggestion for sample selection and handling is good advice for life:</p>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjtCBc74yh3XaCcaBr38JrHbvkY6U63_tbBxyjP1sQJ0SBhqEasQwh7Nct8s4b0oRmXDClKlTOt-7bCnMreGr2SRYkqQsH-NLiV8wm0Flns7hqTLgyZ9R-3yB5WnahwTyI6giDEOeq3TOg/s1600/student_samples.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjtCBc74yh3XaCcaBr38JrHbvkY6U63_tbBxyjP1sQJ0SBhqEasQwh7Nct8s4b0oRmXDClKlTOt-7bCnMreGr2SRYkqQsH-NLiV8wm0Flns7hqTLgyZ9R-3yB5WnahwTyI6giDEOeq3TOg/s568/student_samples.jpg" data-original-width="1600" data-original-height="368" /></a>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-64644982874433973682017-08-03T16:04:00.002-07:002017-08-03T16:05:41.388-07:00Sequencing technologies used for the BABS Genome<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhE0IKl3lAdgyfneh-7mqsxldvDReozH_3a_O4Vg68HLf4kVnJxY-l7ociDVy1DUHIanO6RdwrHDYG5ztcuPNVi2mHLpP-Eg6fCWBvH4b4IDEYl1oxatg_BJTHcy2PQYY5R3Rk148-MLQQ/s1600/Sequencing_Lab.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhE0IKl3lAdgyfneh-7mqsxldvDReozH_3a_O4Vg68HLf4kVnJxY-l7ociDVy1DUHIanO6RdwrHDYG5ztcuPNVi2mHLpP-Eg6fCWBvH4b4IDEYl1oxatg_BJTHcy2PQYY5R3Rk148-MLQQ/s240/Sequencing_Lab.jpg" align="right" style="margin-left:10px" data-original-width="1600" data-original-height="1067" /></a>
Sequencing for the BABS Genome is being performed at the <a href="https://www.ramaciotti.unsw.edu.au/">Ramaciotti Centre for Genomics</a> at UNSW, which is one of Australia’s top sequencing centres and has a long, rich history of genome sequencing.</p>
<p>The Gold Standard for genome assembly is currently to combine three technologies:</p>
<ol>
<li><p>High coverage short read sequencing for accurate base calling of unique regions.</p></li>
<li><p>Long read sequencing for assembling complex and small repetitive regions of the genome.</p></li>
<li><p>Long range sequencing for scaffolding contigs across larger repetitive regions of the genome.</p></li>
</ol>
<p>We will be using a combination of three of these latest technologies for the BABS genome:</p>
<h2 id="illuminanovaseqandhiseqx">Illumina NovaSeq and HiSeq X</h2>
<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgA-APZlWqmaKaBpVoij0JTiBPmqvaO5zz8u9XE-fGOKQEVZVh_Z6Jjn4ArOiI5Hak6ICprqT6_2GJDWCHUs03HUa-C8-UR7QLgx7j-njqGreeA4Gv7fI250NysQ49HB56jS21D0FNPsd4/s1600/NovaSeq1.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgA-APZlWqmaKaBpVoij0JTiBPmqvaO5zz8u9XE-fGOKQEVZVh_Z6Jjn4ArOiI5Hak6ICprqT6_2GJDWCHUs03HUa-C8-UR7QLgx7j-njqGreeA4Gv7fI250NysQ49HB56jS21D0FNPsd4/s320/NovaSeq1.jpg" width="250" align="right" style="margin-left:10px;margin-bottom:20px;margin-top:10px" data-original-width="1070" data-original-height="1600" /></a>
Short read Illumina sequencing is still the starting point for sequencing large (>0.5 Gb) genomes. Although it is impossible to assemble short read data alone into a high-quality genome, it remains the most cost-effective technology in terms of high-quality bases sequenced per dollar. Illumina sequencing struggles with regions of the genome with certain compositional bias and short read assembly fails at repetitive regions. Nevertheless, it is possible to get a useful assembly of a large portion of the “unique” genome, which includes most of the protein-coding genes.</p>
<p>For the 2017 BABS genome, we are using two of the latest - and most cost-effective - Illumina sequencing platform: the HiSeq X (XTen) and new HiSeq NovaSeq. These machines have a phenomenal output per run. The NovaSeq is being used for pure Illumina sequencing, whereas the HiSeq X is being used for the sequencing component of the <a href="#xgenomicschromiumlinkedreads">10X Genomics Linked Read sequencing</a> (below).</p>
<h2 id="pacbiosequel">PacBio Sequel</h2>
<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAW7wiWydyzMWGSpsLaJ6GovN3GvDr7A11jQI180DX-iQEEnofah_L_ihkMuYdv6NdUHus5Yx06CD0IbM84I5aLGNtE4FttdnG6R3ipDt08bV0QJ4FiPYUXzXncVGgTeR2bvQzItx_2fk/s1600/Sequel2.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAW7wiWydyzMWGSpsLaJ6GovN3GvDr7A11jQI180DX-iQEEnofah_L_ihkMuYdv6NdUHus5Yx06CD0IbM84I5aLGNtE4FttdnG6R3ipDt08bV0QJ4FiPYUXzXncVGgTeR2bvQzItx_2fk/s320/Sequel2.jpg" width="250" align="right" style="margin-left:10px;margin-bottom:10px" data-original-width="1070" data-original-height="1600" /></a>
Whole genome sequencing and assembly has been revolutionised by the development of long read sequencing technologies by Pacific Biosciences (PacBio) and Oxford Nanopore (MinION). With typical read lengths a hundred times longer than Illumina reads, long read sequencing enables resolution of many of the shorter repetitive regions in the genome.</p>
<p>Long read sequencing is still comparably expensive and the budget does not stretch for a pure PacBio assembly this year. However, we will be getting some sequencing done on the new PacBio Sequel, which will help with scaffolding Illumina contigs. We also hope to be able to generate a pure PacBio mitochondrial genome; mitochondria are present in multiple copies per cell, which effectively increases the depth of coverage!</p>
<h2 id="xgenomicschromiumlinkedreads">10X Genomics Chromium Linked Reads</h2>
<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1QXwJbaA-N6HbvlyITiPs-V8uaMA6NF3ak_yg4NdG4rd_wG-wMdTMR1jYkE4b_dqsRSjWcdktGbO8qsrOzXhqq-tkdDn9tAOMs5S8IM_1sHpfG2jC4ue7DcoalE98BmCbA5-WzH27z9o/s1600/Chromium_10X_sq.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1QXwJbaA-N6HbvlyITiPs-V8uaMA6NF3ak_yg4NdG4rd_wG-wMdTMR1jYkE4b_dqsRSjWcdktGbO8qsrOzXhqq-tkdDn9tAOMs5S8IM_1sHpfG2jC4ue7DcoalE98BmCbA5-WzH27z9o/s250/Chromium_10X_sq.jpg" data-original-width="1023" data-original-height="1022" align="right" style="margin-left:10px;margin-bottom:20px;margin-top:10px" /></a>
Due to the cost (and DNA requirements) of long read sequencing, there has been considerable effort in recent years to combine cost-effective Illumina short read sequencing with additional experimental approaches to leverage long-range information. The long range service offered by the Ramaciotti Centre is 10X Genomics Chromium linked read sequencing. Unlike PacBio or MinION, this does not contiguously sequence a long DNA molecule. Instead, it uses a clever barcoding system to link short reads back to their DNA molecule of origin. 10X Genomics software then uses this linkage to regenerate pseudo-long-reads that can be used for both genome assembly and haplotype phasing.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-88573264127686386062017-07-28T04:24:00.002-07:002017-07-28T04:24:58.095-07:00What would YOU do with six billion sequencing reads?<table border=0>
<tr><td align="center">
<a href="https://babsgenome.blogspot.com.au/p/technology.html">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjl8Q_XtSIeoCadoxfhs94DpIQC3gOKFqNmMHtAf82PpXfCCvapyzKZm2VzIuEx6sUVn1Io2tUAApwxUXUMrtCo7W9w0MsMJe6_uRvTmK5RS4YyaTP9GqfF0Ut3MYV5Voqd88PerclyqZQ/s330/NovaSeq1.jpg.jpg'); width: 220px; height: 270px; box-shadow: 0 0 8px 8px white inset; padding-bottom: 0px;"> </h3>
</a>
</td><td></td><td>
<p>The <a href="https://www.ramaciotti.unsw.edu.au/">Ramaciotti Centre for Genomics</a>, where we get all the sequencing done for the BABS Genome, is <a href="https://www.ramaciotti.unsw.edu.au/info-centre/news">holding a competition</a> to win a full sequencing run on their new NovaSeq 6000. This is one of <a href="https://babsgenome.blogspot.com.au/p/technology.html">the technologies</a> we are using for our snake genomes - in fact, our three tiger snakes were part of the very first sequencing run on the new machine.</p>
<p>The capacity of this thing is awesome. In addition to the three snake samples, we had three cane toads as part of the ongoing [cane toad genome project] and, for a control, sequenced <a href="http://edwardslab.blogspot.com.au/2015/08/the-smrt-way-to-sequence-yeast-genome.html">one of our yeast strains</a> about 10,000 times!</p>
</td></tr>
</table>
<h2 id="thecompetition">The Competition</h2>
<blockquote>
<h3 id="novaseqminigranthowwouldyouuse3billionreads">NovaSeq Mini Grant – How would you use 3 billion reads?</h3>
<p>To celebrate the opening of our new genomics facility we are pleased to announce a mini grant valued up to $28,000. Researchers with innovative, collaborative projects are invited to submit a 250-word application outlining how 3 billion reads can be utilised to advance their research. The winner will receive an Illumina NovaSeq 6000 S2 100bp PE run (up to 3.3B reads/660Gb), with heavily subsidised library construction. Submit your entry by completing an <a href="http://www.ramaciotti.unsw.edu.au/wp-content/uploads/2017/07/RAMAC_NovaSeq_Mini_Grant_July_2017.pdf">application form</a> and emailing it to Nextgenseq@unsw.edu.au with the subject heading “NovaSeq mini grant”. Terms and conditions apply.</p>
</blockquote>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-55301511172138794912017-07-24T06:31:00.000-07:002017-08-03T16:25:54.378-07:00We're sequencing snakes! (But the competition's still on...)<p>Today was the first <a href="http://www.handbook.unsw.edu.au/undergraduate/courses/2017/BABS3291.html">BABS3291 Genes, Genomes and Evolution</a> lecture and the official opening of the new <a href="https://www.ramaciotti.unsw.edu.au/">Ramaciotti Centre for Genomics</a> labs in the shiny new E26 Bioscience South building at UNSW. This seemed like an appropriate day to reveal the chosen organisms for the BABS2017 Genome.</p>
<p>And the answer is... two snake species!</p>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh44osbxVu0ZDFA3rpCEfJTRDT0b12-ALJ7zBM3BHXXsfDZwjnOHna4XYBf7Mzc5rvz6y6a54rr2mtH62eq1U-n93GC1Y42GbOG6Y7z6T97m6AixmIkhoOqPnY01vcLktWxcMURgJCc6Bg/s1600/Eastern_Tiger_Snake_sq.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh44osbxVu0ZDFA3rpCEfJTRDT0b12-ALJ7zBM3BHXXsfDZwjnOHna4XYBf7Mzc5rvz6y6a54rr2mtH62eq1U-n93GC1Y42GbOG6Y7z6T97m6AixmIkhoOqPnY01vcLktWxcMURgJCc6Bg/s284/Eastern_Tiger_Snake_sq.jpg" data-original-width="1188" data-original-height="1188" /></a>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhU7Q2yKCn-Hi85iFR0pre2RCNt-JQiovXdaLguQFzHrPg5VNjxFEhmO2EeBeidF1OkwjY6WlOMwDixkJw40rIHUkoZSCf9QWY_rhm3OuiQXyWzxtf6xxqOAs0xGgBmzVxZpum9tJnrLeA/s1600/brown_snake.JPG" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhU7Q2yKCn-Hi85iFR0pre2RCNt-JQiovXdaLguQFzHrPg5VNjxFEhmO2EeBeidF1OkwjY6WlOMwDixkJw40rIHUkoZSCf9QWY_rhm3OuiQXyWzxtf6xxqOAs0xGgBmzVxZpum9tJnrLeA/s284/brown_snake.JPG" data-original-width="1600" data-original-height="1600" /></a>
<p>And not just any snakes… the Tiger Snake (left) and Brown snake (right, narrowly avoided by my postdoc Åsa and her partner!) are two of the most deadly snakes in the world. More information will follow in future posts.</p>
<p>Data from the BABS Genome is going to form the core of the seven-week genomics bioinformatics practical at the heart of the coursework for BABS3291. This obviously meant that we needed to start generating data before the course started. We’re still keen to find out what <em>you</em> would like sequenced, though, and <a href="https://goo.gl/forms/MJ8Bb84wXDptZYFj2">the BABS Genome competition</a> remains open for now. Who knows, you may help pick the next genome we do!</p>
<h2 id="photocredits">Photo Credits</h2>
<ul>
<li><p><a href="https://en.wikipedia.org/wiki/Tiger_snake#/media/File:Eastern_Tiger_Snake.jpg">Tiger Snake</a>: Teneche - <a href="http://creativecommons.org/licenses/by-sa/3.0">CC BY-SA 3.0</a>. Location: Banyule Flats Reserve, Melbourne, Victoria.</p></li>
<li><p>Brown Snake: Patrick Dessi. Location: Booroomba Rocks, Namadgi National Park, ACT, Australia.</p></li>
</ul>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-84028980507173300672017-07-17T05:29:00.000-07:002017-07-17T18:50:12.384-07:00One week to go!<p>Official launch date for the BABS Genome Project is <strong>Monday 24th July</strong> to coincide with the start of <a href="http://www.handbook.unsw.edu.au/undergraduate/courses/2017/BABS3291.html">BABSS3291 Genes, Genomes and Evolution</a> and the official reopening of the <a href="https://www.ramaciotti.unsw.edu.au/">Ramaciotti Centre for Genomics</a> in its new home in <strong>E26 Bioscience South</strong> and UNSW.</p>
<p>It’s not too late to <a href="https://goo.gl/forms/Z7roYDeuPDFBCsdo1">enter the competition</a>!</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-2968377684197980482017-06-28T16:16:00.000-07:002017-07-04T02:53:19.820-07:00We're not quite there yet!If you have stumbled across this page, then welcome! The BABS Genome Project has not been officially launched yet but we'll be pre-populating this site with some of the background and early data analysis in the meantime. Feel free to poke around and please report anything odd that you spot!Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-32689843812574000562017-06-25T22:03:00.000-07:002017-07-25T22:10:11.990-07:00Join us on Twitter!<p>The BABS Genome is now on Twitter, <a href="https://twitter.com/babsgenome">@BABSGenome</a>. Follow us for the latest news and updates:</p>
<a href="https://twitter.com/BABSGenome" class="twitter-follow-button" data-size="large" data-show-count="false">Follow @BABSGenome</a><script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-16246797454401398482017-05-21T05:13:00.000-07:002017-07-16T05:27:16.490-07:00Contenders for the 2017 BABS Genome<p>The BABS Genome Project is a bit different from most genome sequencing efforts, which generally start with an organism of interest. Instead, we are crowd-sourcing what we should sequence, with a few constraints:</p>
<ul>
<li>It should be an iconic Australian species.</li>
<li>It should not already have its genome sequenced.</li>
<li>We should be able to generate a reasonable draft genome within budget <a href="http://babsgenome.blogspot.com.au/p/technology.html">using available technology</a>.</li>
<li>We need ready access to samples, from which high molecular weight DNA can be extracted.</li>
</ul>
<a href="https://goo.gl/forms/yzDc1kEDecsspciL2" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkt1dRSLNwKzQLB_u68IYquSYjTuQVmfK44KihA2Lxu08vZNMYF-CjYzlDqZl4hiIDx1FsPv1uJi6dgM9Ayvuyznti5l8jjDTLyh1Oy2UCFfJweOQhPHxgTTm14QPaSD3J5Ru5q2tNzx8/s568/BABSGenomeHeaderLogo.png"/></a>
<p>The current organisms <a href="https://goo.gl/forms/Z7roYDeuPDFBCsdo1">under consideration</a> are:</p>
<table border=0>
<tr><td align="center">
<a href="https://en.wikipedia.org/wiki/Eastern_brown_snake#/media/File:Eastern_Brown_Snake_-_Kempsey_NSW.jpg">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8q6HukNNgG-da3BrkaA9Vp18Zoqe424eiei1vqGMvjvETM899xUZxsQQbUw4oSvYCaOJmK-HdXq-lTfEGE5UHIjDs9egqo5dYK8zsWNhDQ3iRDI-RLYpFt51ndtlymy8Zr4opeLpIMW8/s150/Eastern_Brown_Snake_-_Kempsey_NSW.jpg'); width: 100px; height: 150px; box-shadow: 0 0 8px 8px white inset; margin-bottom:0 px"> </h3>
</a>
</td><td>
<h2>Eastern brown snake</h2>
<p>Despite its rather dull name and appearance, the <a href="https://en.wikipedia.org/wiki/Eastern_brown_snake#/">Eastern Brown Snake</a> is top of <a href="http://www.australiangeographic.com.au/topics/science-environment/2012/07/australias-10-most-dangerous-snakes/">Australian Geographic’s “Australia’s 10 most dangerous snakes”</a> and is the world’s <a href="https://en.wikipedia.org/wiki/Venomous_snake">second-most venomous terrestrial snake</a>.</p>
</td></tr>
<tr><td align="center">
<a href="http://www.australiangeographic.com.au/topics/science-environment/2012/07/gallery-10-most-dangerous-snakes-in-australia/10-most-dangerous-snakes-in-australia_mainland-tiger-snake/">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDFe31QvhkGh7SZlS7CceQVxCqJWSkUmvvqdnnCD-67q-UcB7wCzeeHT7Mo1TQXv_uqqrVewZizLoYtR7krcc5afxjSBxPu0NgBrPND83R8YBROdszmcllHkNoFWgbyi50ADRCJE8ijwM/s258/tiger-snake-Notechis_ater.jpg'); width: 200px; height: 150px; box-shadow: 0 0 8px 8px white inset; padding-bottom: 0px;"> </h3>
</a>
</td><td>
<h2>Tiger snake</h2>
<p>One of the more visually striking species, the <a href="https://en.wikipedia.org/wiki/Tiger_snake">Tiger Snake</a> another <a href="https://en.wikipedia.org/wiki/Venomous_snake">venomous snake</a> and third on <a href="http://www.australiangeographic.com.au/topics/science-environment/2012/07/australias-10-most-dangerous-snakes/">Australian Geographic’s “Australia’s 10 most dangerous snakes”</a>.</p>
</td></tr>
<tr><td align="center">
<a href="http://www.spiders.com.au/funnel-web-spider.html">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLhdHYqmwXVgzIUA4ZJJob9L5dW2vcwWwECNJwifTxocGGKyiWgYwTL_TT6YpCX_HiTOGwBV-dxmbQ4BqcE4PhwcLcTEudxHJMK-95EoY5NN6vxE-IqYQwHf-N9iL-bBB530BPt0KqToo/s217/panel-funnel-web-3.gif'); width: 200px; height: 150px; box-shadow: 0 0 8px 8px white inset;" > </h3>
</a>
</td><td>
<h2>Funnel web spider</h2>
<p>The <a href="https://en.wikipedia.org/wiki/Sydney_funnel-web_spider">Funnel web spider</a> is a common venomous spider that tops <a href="http://www.australiangeographic.com.au/topics/wildlife/2012/08/australian-spiders-the-10-most-dangerous/">Australian Geographic’s “Australia’s 10 most dangerous spiders”</a> list.</p>
</td></tr>
<tr><td align="center">
<a href="https://en.wikipedia.org/wiki/Maratus_volans#/media/File:MalePeacockSpider.jpg">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjb-46kPopGNqRJ0JIB6qq3pvfNXFkj5MOg87gjKh8eomnA_0fVZKB_hPICvEpTJGpVgnr3JAq7iKHdeutXL72BUrYKefHWrLIpzVdlBW0QZfknCyd-iBrdm4sRGzeCJ2Deo_ZQrK3cwCU/s171/MalePeacockSpider.jpg'); width: 171px; height: 150px; box-shadow: 0 0 8px 8px white inset;" > </h3>
</a>
</td><td>
<h2>Peacock spider</h2>
<p>The <a href="https://en.wikipedia.org/wiki/Maratus">peacock spider</a> is a small Australian spider famous for <a href="https://www.youtube.com/results?search_query=peacock+spider">videos of its mating dance</a>.</p>
</td></tr>
<tr><td align="center">
<a href="https://en.wikipedia.org/wiki/Amphiprioninae#/media/File:Clown_fish_in_the_Andaman_Coral_Reef.jpg">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjj5tUPpo41ahAHLoaJ_m64r55u7bZGjZkIagDT7BqUEBwDcoK1KWsJHMDgxvOL2dd5gUSINYqvDiIGQHSSEqUkEiTIKwY6vtDYwD0aKBlbmakROcXDZz4toSYUBflJevTS8G5rSzN_Jh8/s224/Clown_fish_in_the_Andaman_Coral_Reef.jpg'); width: 200px; height: 150px; box-shadow: 0 0 8px 8px white inset; margin-bottom:0 px" > </h3>
</a>
</td><td>
<h2>Clownfish</h2>
<p>Made famous by Finding Nemo, the <a href="https://en.wikipedia.org/wiki/Amphiprioninae">clownfish</a> is an iconic tropical fish that lives in the Great Barrier Reef and forms a symbiotic relationship with sea anemones.</p>
</td></tr>
<tr><td align="center">
<a href="http://irukandjijellyfish.com/">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiqrRlbQz1wGbeRt5C5TURgUUL8GIkOhZVkhJ12cHrOQP-5Q0MsM8RkYGfBQmi9znRxOowqjt5rGLym2WdyxZH0w7XUkKobmvAivA__BqgIm4i3hCiguhquaPr-jEAU6z2Z990772DPlJc/s150/irukandji-jellyfish-200802.jpg'); width: 109px; height: 150px; box-shadow: 0 0 8px 8px white inset; margin-bottom:0 px" > </h3>
</a>
</td><td>
<h2>Irukandji jellyfish</h2>
<p>Another one on the “Australia’s most deadly” list, the <a href="https://en.wikipedia.org/wiki/Irukandji_jellyfish">Irukandji jellyfish</a> is a small venomous <a href="https://en.wikipedia.org/wiki/Box_jellyfish">Box jellyfish</a> with sufficient toxicity to kill a person.</p></td></tr>
<tr><td align="center">
<a href="http://www.onychophora.com/">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHHsbzWx0gBA2qAjhu3Ac0eMrhR0Gsel6KVzaZdPeD-e_ZaKmHQHQOf4tQ5LovTSziIrUdZTvNN-tawGG4TQwpNtNZVIfoZrZ0nkIGkyDEoxhoYZooWqt8IX0a_lnmhGWbOGTp6TSD0T8/s226/Onychophora.png'); width: 200px; height: 150px; box-shadow: 0 0 8px 8px white inset; margin-bottom:0 px" > </h3>
</a>
</td><td>
<h2>Velvet Worm</h2>
<p><a href="https://en.wikipedia.org/wiki/Onychophora">Velvet worms</a> are bizarre slime-squirting carnivorous animals with interesting reproductive methods.</p>
</td></tr>
<tr><td align="center">
<a href="https://en.wikipedia.org/wiki/Dryococelus_australis#/media/File:Dryococelus_australis_02_Pengo.jpg">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXSANV8ufUjiGHEj7DQs3Pgs7dmwGBsJ8DYnG5MRLVhRBgB2plclcKhWG2Dd2OrSKV24a3RXyorvnjM4k1s8qEvf32ivHX4UwU9OFR5cn3-2PbxyZql6C3AzpXWfLKqQSuw1GOnIRxWGc/s150/800px-Dryococelus_australis_02_Pengo.jpg'); width: 74px; height: 150px; box-shadow: 0 0 8px 8px white inset;"> </h3>
</a>
</td><td>
<h2>Lord Howe Island Stick Insect</h2>
<p>The <a href="https://en.wikipedia.org/wiki/Dryococelus_australis">Lord Howe Island Stick Insect</a> is one of the rarest insects in the world and was thought extinct for over 80 years.</p>
</td></tr>
<tr><td align="center">
<a href="https://en.wikipedia.org/wiki/Yellow-tailed_black_cockatoo#/media/File:Calyptorhynchus_funereus_(male)_-Wamboin-8.jpg">
<h3 style="background-image: url('https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhFJq6OLrTxE4kOXpPTAO-rhI4pyRWB617VEowCEqhxBoPpdphCOcgqMUGinQCITQjEIJAVpEU8mKNYsO4wT874AI72q6IzH34HTjO91CudMtnV1uPTkxQWJ0HCAElwU4TjxoTliJRvoOY/s150/Calyptorhynchus_funereus_%2528male%2529_-Wamboin-8.jpg'); width: 113px; height: 150px; box-shadow: 0 0 8px 8px white inset; margin-bottom:0 px" > </h3>
</a>
</td><td>
<h2>Black cockatoo</h2>
<p>The <a href="https://en.wikipedia.org/wiki/Yellow-tailed_black_cockatoo">Yellow-tailed black cockatoo</a> is not as well know as its sulphur-crested cousin but is another iconic species of south-east Australia. Black cockatoos are under threat from habitat loss and illegal trading, making it a key conservation target.</p>
</td></tr>
</table>
<p>To <a href="http://babsgenome.blogspot.com.au/p/get-involved.html">get involved</a>, please complete <a href="https://goo.gl/forms/Z7roYDeuPDFBCsdo1">the BABS Genome survey</a>. (BABS students might win a prize!) To add to this list, complete the survey or <a href="http://babsgenome.blogspot.com.au/p/contact.html">get in touch</a>.</p>
<h2 id="photocredits">Photo Credits</h2>
<p><a href="https://en.wikipedia.org/wiki/Eastern_brown_snake#/media/File:Eastern_Brown_Snake_-_Kempsey_NSW.jpg">Brown snake</a> - <a href="https://commons.wikimedia.org/wiki/User:Poyt448">Peter Woodard</a> |
<a href="http://www.australiangeographic.com.au/topics/science-environment/2012/07/gallery-10-most-dangerous-snakes-in-australia/10-most-dangerous-snakes-in-australia_mainland-tiger-snake/">Tiger snake</a> - Australian Geographic |
<a href="http://www.spiders.com.au/funnel-web-spider.html">Funnel web spider</a> - Spiders.com.au |
<a href="https://en.wikipedia.org/wiki/Maratus_volans#/media/File:MalePeacockSpider.jpg">Peacock spider</a> - Jurgen Otto [<a href="http://creativecommons.org/licenses/by-sa/2.0">CC-BY-SA 2.0</a>] |
<a href="https://en.wikipedia.org/wiki/Amphiprioninae#/media/File:Clown_fish_in_the_Andaman_Coral_Reef.jpg">Clownfish</a> – <a href="https://commons.wikimedia.org/wiki/User:Ritiks">Ritiks</a> [<a href="http://creativecommons.org/licenses/by-sa/3.0">CC-BY-SA 3.0</a>] |
<a href="http://irukandjijellyfish.com/">Irukandji jellyfish</a> - irukandjijellyfish.com |
<a href="http://www.onychophora.com/">Velvet worm</a> - onychophora.com © I.S. Oliveira, L. Hering & G. Mayer |
<a href="https://en.wikipedia.org/wiki/Dryococelus_australis#/media/File:Dryococelus_australis_02_Pengo.jpg">Lord Howe Stick Insect</a> - Wikipedia [<a href="http://creativecommons.org/licenses/by-sa/3.0">CC-BY-SA 3.0</a>] |
<a href="https://en.wikipedia.org/wiki/Yellow-tailed_black_cockatoo#/media/File:Calyptorhynchus_funereus_(male)_-Wamboin-8.jpg">Yellow-tailed black cockatoo</a> – <a href="https://www.flickr.com/photos/16520061@N08">David Cook Wildlife Photography</a> [<a href="http://creativecommons.org/licenses/by-sa/2.0">CC-BY-SA 2.0</a>]</p>
Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-7128301431472585827.post-70036299065253265382017-04-20T05:49:00.000-07:002017-06-25T02:02:44.235-07:00The BABS Genome Project<p>The BABS Genome is a student-centred initiative of the <a href="https://www.babs.unsw.edu.au/">School of Biotechnology and Biomolecular Science (BABS)</a> to sequence and assemble a eukaryotic genome for use in teaching and outreach. Genomic data will be analysed as part of the educational experience for <a href="http://www.handbook.unsw.edu.au/undergraduate/courses/2017/BABS3291.html">BABS3291: Genes, Genomes and Evolution</a>. Sequencing will be performed with the latest technologies through the <a href="https://www.ramaciotti.unsw.edu.au">Ramaciotti Centre for Genomics</a> at UNSW.</p><br />
Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0