.huge[The Humble Guinea Pig]

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# .huge[The Humble Guinea Pig]
## …Cute, Furry and Deserving of a Better Genome Assembly…
### <div class="line-block"><a href="http://sirselim.github.io/">Miles Benton</a><br />
Senior Scientist Bioinformatics<br />
Human Genomics, Institute of Environmental Science and Research (ESR)<br />
<br />
.large[Queenstown Research Week, Queenstown, 5<small><sup>th</sup></small> September 2019]<br />
<br />
<br />
.center[<img src="images/ESR_Logo_SFC_reversed.png" style="width: 30%;"/>]</div>

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# .center[Advocate for reproducible research...]

## .center[Where possible my presentations and code are available online]

<br />

<p>
.center[
<img src="images/github_logo.png" style="width: 520px; margin-right: 1%; margin-top: 1.5em;"/>
<img src="images/sirselim_qrcode.png" style="width: 202px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>

<br />

.center[[sirselim.github.io/presentations](http://sirselim.github.io/presentations)]

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# Why guinea pig genomes?

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<p>
.center[
<img src="images/article.png" style="width: 820px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>

.small[.center[(*link to article [here](https://tinyurl.com/yy9fuw95)*)]]

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<p>
.center[
<img src="images/GuineaPig.jpg" style="width: 720px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>

## "We deserve a decent reference after everything we've been through!"

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<p>
.center[
<img src="images/promethion.jpg" style="width: 420px; margin-right: 1%; margin-top: 1.5em; border: 3px solid white;"/>
<img src="images/NovaSeq6000.jpg" style="width: 320px; margin-right: 1%; margin-top: 1.5em; border: 3px solid white;"/>
]
</p>

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<br>

<span style="color:#3498DB">**Long read sequencing**</span>

* 3 out-bred females

<br>

--

<span style="color:#3498DB">**Short read sequencing**</span>

* 6 animals
  * 3 females (same animals as above)
  * 3 males (a brother of each female)

<br>

--

... what about the Y chr? ...

--

* FISH for Y
* sequence on our in-house minION
* student project

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# Slight segue...

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background-image: url("images/titan.jpg")
background-size: cover

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# GPU benchmarking*

We have been collecting some metrics and thoughts [here](https://esr-nz.github.io/gpu_basecalling_testing/gpu_benchmarking.html).

<br>

_*<b>spoiler</b>: it's MUCH faster!!_

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<br>
<br>

# Cute, Furry and Deserving of a Better Genome Assembly...

<br>
<br>

--

## ...unfortunately not quite yet...

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# Liver tissue is being "fun"...

<p>
.center[
<img src="images/not_good_1.png" style="width: 760px;"/>
]
</p>

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# Liver tissue is being "fun"...

<p>
.center[
<img src="images/better_1.png" style="width: 760px;"/>
]
</p>

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# Liver tissue is being "fun"...

<p>
.center[
<img src="images/not_good_2.png" style="width: 760px;"/>
]
</p>

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# Liver tissue is being "fun"...

<p>
.center[
<img src="images/better_2.png" style="width: 760px;"/>
]
</p>

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# Liver tissue is being "fun"...

<p>
.center[
<img src="images/not_good.png" style="width: 760px;"/>
]
</p>

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# Liver tissue is being "fun"...

<p>
.center[
<img src="images/better.png" style="width: 760px;"/>
]
</p>

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# What can I tell you?

--

.large[We have a very high coverage complete mt genome...]

<br>

--

<br>

1. downsample ([fastx-sample.pl](https://gitlab.com/gringer/bioinfscripts/blob/master/fastx-sample.pl) David Eccles)

2. mapping - [minimap2](https://github.com/lh3/minimap2)

3. assembly - [miniasm](https://github.com/lh3/miniasm)

4. consensus
```sh
# GFA to fasta
awk '$1 ~/S/ {print ">"$2"\n"$3}' reads.gfa > reads.fasta
```

5. re-map - [minimap2](https://github.com/lh3/minimap2)

6. polish - [racon](https://github.com/lbcb-sci/racon)

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<p>
.center[
<img src="images/Cpor_assembly_k12_001.png" style="width: 590px;"/>
]
</p>

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<p>
.center[
<img src="images/Cpor_assembly_k8_001.png" style="width: 590px;"/>
]
</p>

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<p>
.center[
<img src="images/Cpor_mtDNA_endRepeat.png" style="width: 590px;"/>
]
</p>

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<p>
.center[
<img src="images/assembled_guinea_k12_001.png" style="width: 890px;"/>
]
</p>

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<p>
.center[
<img src="images/stompPlot_Cpor_mtDNA.png" style="width: 990px;"/>
]
</p>

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<p>
.center[
<img src="images/msa_nucl_assembled_gp_Cpor_mtDNA_rotated.png" style="width: 590px;"/>
]
</p>

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<p>
.center[
<img src="images/zoomed.png" style="width: 790px;"/>
]
</p>

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<p>
.center[
<img src="images/stompPlot_utg000001c.png" style="width: 990px;"/>
]
</p>

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# How about some epigenetics?

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<br>

# Facilitating collaboration

* using reproducible research ethos
* creating interactive documents and applications
* empowers data owners to explore their own data

--

## example

RRBS guinea pig liver

* pre-term (n=6) vs term (n=6)
* shiny app to explore data
  * differential meth
  * PCA
  * interactive results tables

--

.center[ Make available via our [internal server](http://leviathan/human_genomics/) and [shinyapps.io](https://www.shinyapps.io). ]

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# Guinea Liver RRBS

<p>
.pull-left[
<img src="images/pheatmap_dfmeth_20190903.png" style="width: 690px;"/>
]
</p>

<p>
<br>

<ul>
<br>
<br>
<br>
<li>differential methylation - <a href="https://github.com/al2na/methylKit" target="blank">[methylkit]</a></li>
<br>
<br>
<li>490 CpG sites FDR < 0.05 & >10% diff meth</li>
<br>
<br>
<li>interesting biology / pathways</li>  
</ul>
<br>
<br>
.pull-left[
Experimental Shiny app [here](https://esr-cri.shinyapps.io/methylation_plotting_app/)
]

</p>

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# Where to next?

.large[

* "reboot" the project

* complete mtDNA aside

* explore long-read base modifications

* RRBS: targeted validation

* manuscripts

] 
 
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# Acknowledgements

<div id="images">
    <a href="http://xyz.com/hello">
        <img src="images/max.jpg" style="width: 180px; height: 250px; margin-right: 1%; margin-top: 1.5em; border: 3px solid white;"/>
        <div class="caption"><span style="color:#3498DB">Max Berry (University of Otago)</span></div>
    </a>
    <a href="http://xyz.com/hi">
        <img src="images/donia.jpg" style="width: 180px; height: 250px; margin-right: 1%; margin-top: 1.5em; border: 3px solid white;"/> 
        <div class="caption"><span style="color:#3498DB">Donia Macartney-Coxson (ESR)</span></div>
    </a>
</div>

.pull-left[.medium[
.center[Rebecca Dyson (University of Otago)]

.center[<img src="images/UoO_logo.png" style="height: 90px; "/>]

]]

.pull-right[.medium[
.center[Jane Clapham (ESR)

Joep de Ligt (ESR)

David Eccles (Malaghan Institute)]
]]