# .large[The disruptive nature of portable sequencing for community empowerment… and GPUs]
### <div class="line-block">Genomics Aotearoa Friday Seminar Series, 9<small><sup>th</sup></small> April 2021<br />
.large[<b>Dr Miles Benton</b>]<br />
<br />
<b>Human Genomics</b><br />
<b>Institute of Environmental Science and Research <a href="www.esr.cri.nz">(ESR)</a></b><br />
<b>Aotearoa</b> (New Zealand)</div>

---

<div>
<style type="text/css">.xaringan-extra-logo {
width: 138px;
height: 87px;
z-index: 0;
background-image: url(https://upload.wikimedia.org/wikipedia/commons/6/66/ESR_SFC_logo.png);
background-size: contain;
background-repeat: no-repeat;
position: absolute;
right:1.5em;bottom:1px;
}
</style>
<script>(function () {
  let tries = 0
  function addLogo () {
    if (typeof slideshow === 'undefined') {
      tries += 1
      if (tries < 10) {
        setTimeout(addLogo, 100)
      }
    } else {
      document.querySelectorAll('.remark-slide-content:not(.title-slide):not(.inverse):not(.hide_logo)')
        .forEach(function (slide) {
          const logo = document.createElement('a')
          logo.classList = 'xaringan-extra-logo'
          logo.href = 'https://www.esr.cri.nz/'
          slide.appendChild(logo)
        })
    }
  }
  document.addEventListener('DOMContentLoaded', addLogo)
})()</script>
</div>

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

## .center[Where possible all 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 />

<footer class="pv3 ph3 ph5-ns tc">
  <a class="link near-black hover-blue dib h2 w2 mr3" href="https://github.com/sirselim" title="GitHub">
    <svg fill="currentColor" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" fill-rule="evenodd" clip-rule="evenodd" stroke-linejoin="round" stroke-miterlimit="1.414"><path d="M8 0C3.58 0 0 3.582 0 8c0 3.535 2.292 6.533 5.47 7.59.4.075.547-.172.547-.385 0-.19-.007-.693-.01-1.36-2.226.483-2.695-1.073-2.695-1.073-.364-.924-.89-1.17-.89-1.17-.725-.496.056-.486.056-.486.803.056 1.225.824 1.225.824.714 1.223 1.873.87 2.33.665.072-.517.278-.87.507-1.07-1.777-.2-3.644-.888-3.644-3.953 0-.873.31-1.587.823-2.147-.083-.202-.358-1.015.077-2.117 0 0 .672-.215 2.2.82.638-.178 1.323-.266 2.003-.27.68.004 1.364.092 2.003.27 1.527-1.035 2.198-.82 2.198-.82.437 1.102.163 1.915.08 2.117.513.56.823 1.274.823 2.147 0 3.073-1.87 3.75-3.653 3.947.287.246.543.735.543 1.48 0 1.07-.01 1.933-.01 2.195 0 .215.144.463.55.385C13.71 14.53 16 11.534 16 8c0-4.418-3.582-8-8-8"/></svg>
  </a>
  <a class="link hover-blue near-black dib h2 w2 mr3" href="https://twitter.com/miles_benton" title="Twitter">
    <svg fill="currentColor" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" fill-rule="evenodd" clip-rule="evenodd" stroke-linejoin="round" stroke-miterlimit="1.414"><path d="M16 3.038c-.59.26-1.22.437-1.885.517.677-.407 1.198-1.05 1.443-1.816-.634.375-1.337.648-2.085.795-.598-.638-1.45-1.036-2.396-1.036-1.812 0-3.282 1.468-3.282 3.28 0 .258.03.51.085.75C5.152 5.39 2.733 4.084 1.114 2.1.83 2.583.67 3.147.67 3.75c0 1.14.58 2.143 1.46 2.732-.538-.017-1.045-.165-1.487-.41v.04c0 1.59 1.13 2.918 2.633 3.22-.276.074-.566.114-.865.114-.21 0-.416-.02-.617-.058.418 1.304 1.63 2.253 3.067 2.28-1.124.88-2.54 1.404-4.077 1.404-.265 0-.526-.015-.783-.045 1.453.93 3.178 1.474 5.032 1.474 6.038 0 9.34-5 9.34-9.338 0-.143-.004-.284-.01-.425.64-.463 1.198-1.04 1.638-1.7z" fill-rule="nonzero"/></svg>
  </a>
  <a class="link hover-blue near-black dib h2 w2 mr3" href="https://scholar.google.co.nz/citations?user=iEhBavEAAAAJ&hl=en" title="Google Scholar">
    <svg fill="currentColor" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" fill-rule="evenodd" clip-rule="evenodd" stroke-linejoin="round" stroke-miterlimit="1.414"><path d="M12 24a7 7 0 1 1 0-14 7 7 0 0 1 0 14zm0-24L0 9.5l4.838 3.94A8 8 0 0 1 12 9a8 8 0 0 1 7.162 4.44L24 9.5z" fill-rule="nonzero"/></svg>
  </a>
  <a class="link hover-blue near-black dib h2 w2 mr3" href="http://orcid.org/0000-0003-3442-965X" title="ORCID">
    <svg fill="currentColor" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" fill-rule="evenodd" clip-rule="evenodd" stroke-linejoin="round" stroke-miterlimit="1.414"><path d="M12 0C5.372 0 0 5.372 0 12s5.372 12 12 12 12-5.372 12-12S18.628 0 12 0zM7.369 4.378c.525 0 .947.431.947.947s-.422.947-.947.947a.95.95 0 0 1-.947-.947c0-.525.422-.947.947-.947zm-.722 3.038h1.444v10.041H6.647V7.416zm3.562 0h3.9c3.712 0 5.344 2.653 5.344 5.025 0 2.578-2.016 5.025-5.325 5.025h-3.919V7.416zm1.444 1.303v7.444h2.297c3.272 0 4.022-2.484 4.022-3.722 0-2.016-1.284-3.722-4.097-3.722h-2.222z" fill-rule="nonzero"/></svg>
  </a>
</footer>

---
layout: false
class: middle hide_logo

---
class: middle

# Who are we?

.pull.right[
.large[<span style="color:#3498DB">**You may have seen recently**...</span>]
]

---
class: top

# Genomics in NZ's pandemic response

### A sequencing success story made possible by the awesome [**Una Ren**](https://twitter.com/sciolato), [**Matt Storey**](https://twitter.com/mathstorey) & [**Joep de Ligt**](https://twitter.com/joepdl)

<article class="cf">
  <div class="fl w-50 bg-white tc">
    <img src="images/JN_FirstGenome.PNG" style="width: 80%; margin-right: 1%; margin-top: 0em;"/>
  </div>
  <div class="fl w-40 bg-white tc">
    <p style="text-align:center"> Give us some time and money and we'll demonstrate what this technology can do. <br />  <br />  <br /> </p>
  </div>
  
  <div class="fl w-40 bg-white tc">
    <img src="images/NZChiefSCIAdvisor.PNG" style="width: 100%; margin-right: 1%; margin-top: 0em;"/>
  </div>
</article>

---
layout: false
class: middle inverse

background-image: url("https://cdn.vox-cdn.com/thumbor/llQlREwACaitewdPcLm5HzWT_g0=/0x1:1100x734/920x613/filters:focal(0x1:1100x734):format(webp)/cdn.vox-cdn.com/imported_assets/1507663/DNA-sequence.jpg")
background-size: cover

???

DNA - A, T, C, G
Part of all 'living' things

---

# A snapshot of the Human Genomics group

* **Independent research**
  * type-2 diabetes & obesity (genomics, epigenetics, protein 'omics)
  * Guinea pigs! (<span style="color:#3498DB"><b>Max Berry, University of Otago</b></span>)
  * empowering people to explore and interpret their data

<br>

* **Clinical diagnostics through genetics**
  * Contract(s) with CCDHB <span style="color:#3498DB"><b>Wellington Regional Genetics Lab</b></span>
  * Providing support to CCDHB for Clinical Genomics GA project (<span style="color:#3498DB"><b>Stephen Robertson</b></span>)

<br>

* **Clinical research**, in collaboration with local clinician (<span style="color:#3498DB"><b>Richard Carroll</b></span>) - hyperparathyroidism
  * sequencing 100 exomes
  * engaging clinicians from other DHBs
  * exploring the replacement of gene panels with exome/genome

---
class: middle center

# A big part of what we do is sequencing

---
layout: false
class: middle

<p>
.center[
<img src="https://www.illumina.com/content/dam/illumina-marketing/images/decade-in-sequencing/decade-in-sequencing-320-web-graphic.jpg" style="width: 820px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>

.small[.center[
(image source: [illumina.com](https://www.illumina.com/techniques/sequencing/dna-sequencing.html))
]]

???

I used the word portable in my previous slide, this is not a phrase one would attribute to machines from Illumina / PacBio.

These things are huge! ... and expensive.

---
class: middle

> *"Soon, It Will Cost Less To Sequence A Genome Than To Flush A Toilet -- And That Will Change Medicine Forever"*

<p>
.center[
<img src="images/seqCost.png" style="width: 620px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>

.small[.center[
(image source: [https://www.businessinsider.com.au/super-cheap-genome-sequencing](https://www.businessinsider.com.au/super-cheap-genome-sequencing-by-2020-2014-10))
]]

---
class: top

# Can we speed things up?

<b>Thanks to eResearch 2020<b> ...enter [Nvidia Clara Parabricks](https://www.nvidia.com/en-us/docs/parabricks/)

---
class: middle

.center[
<img src="images/parabricks_pipelines.png" style="width: 70%; margin-right: 1%; margin-top: 0em;"/>
]

<br>

.center[[www.nvidia.com/en-us/healthcare/clara-parabricks/](https://www.nvidia.com/en-us/healthcare/clara-parabricks/)]

---

# How much does that matter?

### Identical pipelines with a slight difference...

<article class="cf">
  <div class="fl w-100 w-50-ns bg-white">
    <ul>
    <li><b>Pipeline [CPU]</b></li>
      <ul>
        <li>Exomes: >100X exome takes between 8-12 hours</li>
        <li>Genomes: ~30X genome takes between 30-48 hours</li>
      </ul>
    </ul>
    <br>
    <ul>
    <li><b>Pipeline [GPU - Parabricks]</b></li>
      <ul>
        <li>Exomes: >100X exome takes between <span style="color:#3498DB"><b>6-12 mins</b></span></b></li>
        <li>Genomes: 100X genome takes <span style="color:#3498DB"><b>~4 hours</b></span></li>
        <br>
        <li>was on 2x V100 GPUs, now also have 2x A100s</li>
      </ul>
    </ul>
  </div>
  <div class="fl w-100 w-50-ns bg-white tc">
    <img src="images/fast-turtle.png" style="width: 70%; margin-right: 1%;"/>
  </div>
</article>

---
class: middle

<br>

.center[[www.nvidia.com/en-us/healthcare/clara-parabricks/](https://www.nvidia.com/en-us/healthcare/clara-parabricks/)]

---
class: middle

---
class: middle

<center>
<a href="https://twitter.com/LeahKem63535098/status/1380108139119267840" target="blank">Fun with Nvidia A100s!!</a>
</center>

---
class: top

# Complete Overhaul! [Leah Kemp]

<br>

<article class="cf">
  <div class="fl w-100 w-50-ns bg-white">
    <br>
    <br>
    <br>
    <ul>
      <li>Alignment and Variant Calling Workflow</li>
        <ul>
          <li><a href="https://github.com/ESR-NZ/human_genomics_pipeline" target="blank">[human_genomics_pipeline]</a></li>
        </ul>
    <br>
    <br>
      <li>Variant Annotation Workflow</li> 
        <ul>
          <li><a href="https://github.com/ESR-NZ/vcf_annotation_pipeline" target="blank">[annotation_pipeline]</a></li>
        </ul>
    </ul>
  </div>
  <div class="fl w-100 w-50-ns bg-white tc">
  <article class="mw5 center bg-white br3 pa3 pa4-ns mv3 ba b--black-10">
    <div class="tc">
      <img src="images/Leah.jpeg" class="br-100 h4 w4 dib ba b--black-05 pa2" title="Photo of team member">
      <h4 class="f3 mb2">Leah Kemp</h4>
      <h4 class="f5 fw4 gray mt0">(ESR)</h4>
    </div>
  </article>
  </div>
</article>

---
class: middle

# Another type of sequencing technology

---
layout: false
class: middle

<p>
.center[
<img src="https://cdn-a.william-reed.com/var/wrbm_gb_food_pharma/storage/images/publications/food-beverage-nutrition/foodnavigator.com/article/2018/03/21/oxford-nanopore-raises-funds-to-support-commercial-expansion/7992741-1-eng-GB/Oxford-Nanopore-raises-funds-to-support-commercial-expansion_wrbm_large.jpg" style="width: 620px; margin-right: 1%; margin-top: 1.5em;"/>
]
</p>

.small[.center[
(image source: [nanoporetech](https://nanoporetech.com/about-us/news/oxford-nanopore-announces-ps100-million-140m-fundraising-global-investors))
]]

???

flongle: ~$500 USD for 5
1 might be enough for a metagenome

minION: $1000

smidgION: still just a concept

gridION: ~$50K

promethION: ~$230K

---
layout: false
class: hide_logo

<a href="https://f1000research.com/slides/8-1947" style="position:absolute; top:625px; left:190px">slide kindly supplied by David Eccles (f1000 presentation)</a>
<a href="https://www.youtube.com/watch?v=CHCAb-PAqUI" style="position:absolute; top:652px; left:190px">"Sequencing DNA with Linux Cores and Nanopores"</a>

???

David's talk and a live demo are linked.

---
layout: false
class: middle hide_logo

<center>
<iframe width="1000" height="562" src="https://www.youtube.com/embed/RcP85JHLmnI" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br />
&copy; Oxford Nanopore Technologies
</center>

---
layout: false
class: middle

# Example squiggle plot

![](https://nanoporetech.github.io/tombo/_images/single_samp.png)

.small[.center[
(image source: [tombo manual](https://nanoporetech.github.io/tombo/plotting.html))
]]

???

What we 'see' when DNA passes through the pores.

---
class: middle

# GPUs accelerate basecalling of Nanopore long-read data (a lot)

<br>

.center[
Nanopore basecalling benchmarking: [link (ESR GitHub)](https://esr-nz.github.io/gpu_basecalling_testing/gpu_benchmarking.html)
]

---
class: middle

# Why GPUs?

* squiggle data lends itself nicely to neural nets
* GPUs are very capable in this space
  - CUDA cores

ESR GPU basecalling benchmarks [(link)](https://esr-nz.github.io/gpu_basecalling_testing/gpu_benchmarking.html)
* Titan RTX & 2x Tesla V100
]

<br>

---
class: middle

# Let's step back a couple of years

.pull.right[
.large[<span style="color:#3498DB">... **a personal story** ...</span>]
]

---
class: middle

<p>
.center[
<img src="images/jamie_sm.jpg" style="width: 330px; margin-right: 1%; margin-top: 1.5em; border: 3px solid white;"/>
<img src="images/jamie_big.jpg" style="width: 334px; margin-right: 1%; margin-top: 1.5em; border: 3px solid white;"/>
]
</p>

---
class: top

# a personal story

* had a lumbar puncture ('9 days' old) 
  * (after being born 8 weeks early)

<br>

* suspected meningitis (bacteria/viral)?
 * told after the fact

<br>

* \>**48 hours** for results return

]

---
class: top

# a personal story

<br>

.large[
* a sample (i.e. blood) taken,
* DNA/RNA extracted/enriched,
* sequencing library prepared,
* nanopore sequencing initiated,
* sequence starts coming in almost instantly,
* **<span style="color:#3498DB">time to first read-match detection <1 hr</span>**

]

<br>

???

Stress how fast and low cost this has the potential to be.

---
class: top

# what are we doing?

* <span style="color:#3498DB">**the idea**</span>

* low cost (< many mobile phones)
  * accessible
  * portable
  * robust (...may have "performed" a drop test...)
  * fun!

--
  
* <span style="color:#3498DB">**example use cases**</span>

* field sequencing (real-time monitoring, forensics, agriculture, waterways, ...)
  * **clinical settings**
  * community outreach / teaching

---
class: middle

# Our experiences with the Xavier [(link)](https://hackmd.io/@Miles/HkumH7sBH)

.pull-left[.right[
<img src="images/IMG_20191021_165639.jpg" style="width: 200px;"/>
<img src="images/IMG_20191025_094614.jpg" style="width: 200px;"/>
]]

.pull-right[.left[
<img src="images/battery_charge.jpg" style="width: 200px;"/>
<img src="images/xavier_in_use.jpg" style="width: 200px;"/>
]]

???

Talk about the Xavier specs:

* 8 core arm 
 * 16 GB of RAM
 * 512 CUDA core and 64 tensor cores
 * 512 GB SSD NVMe

---
class: top

# Benchmarking [(link)<sup>*</sup>](https://gist.github.com/sirselim/2ebe2807112fae93809aa18f096dbb94)

<br>

Most Jetson devices have the ability to be put into different power modes

<br>

<div id="htmlwidget-9e9ea86ed6ddeaef53d8" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-9e9ea86ed6ddeaef53d8">{"x":{"filter":"none","fillContainer":false,"data":[["10W","15W","30W 2 cores","30W 4 cores","30W MAX (8 cores)"],["33.4 mins","14.3 mins","10.8 mins","10.8 mins","7.5 mins"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>Power.mode<\/th>\n      <th>Time<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"t","order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
.small[
***Note:*** this table represents basecalling performed when running on a portable powerbank.
]

???

Why is 10W mode exciting?

We're running in 30W MAX mode for this live demo - running on a portable powerpack.

---
class: top

## Very rough comparison of Nvidia ecosystem<sup>#</sup>

<div id="htmlwidget-7573f7bbe3372dc41045" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-7573f7bbe3372dc41045">{"x":{"filter":"none","fillContainer":false,"data":[["Jetson Nano","Jetson Xavier NX*","Jetson Xavier","Geforce 1080 Ti","Geforce 2080 Ti","Titan RTX","Tesla V100"],["~0.5","6","11","11.3","~13-14","16.3","16.4"],["$99","$399","$699","~$650","~$800-$1000","~$3000","~$8500"],["5-10W","10-15W","10-30W","215W","250W","280W","250W"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>Card<\/th>\n      <th>TFLOPS<\/th>\n      <th>Price<\/th>\n      <th>Power<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"t","order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>

.small[Price in USD]  
.small[<sup>#</sup> a very small selection of what Nvidia offers obviously!]  
.small[\* this can fit in an existing Jetson Nano carrier boards]

???

V100 could rip through this data in a couple of mins, but consider the cost, power, etc.

Xavier NX is exciting, module that can slot into the Nano body [**hold up Nano device**]

---
class: middle

# Community engagement leading to empowerment

.pull.right[
<span style="color:#3498DB">... **a few stories of the journey** ...</span>
]

---

# So how about unlocking it for everyone?

.center[
<img src="images/JB_twitterprofile.png" style="width: 60%; margin-right: 1%; margin-top: 1em;"/>
]

---

# The unboxing and a slight snag

---

# Success

---
class: middle

# A global cast of many

* [***Kenya***] Jean-Bakka Domelevo Entfellner ([@JeanBakaDE](https://twitter.com/JeanBakaDE))

* [***USA***] John Erb-Downward ([@Bombanat](https://twitter.com/bombanat))

* [***Italy***] Luigi Faino ([@lfaino](https://twitter.com/lfaino))

* [***Switzerland***] Jürgen Hench

* [***USA***] Nvidia Clara Team ([Clara AGX site](https://developer.nvidia.com/clara-agx-devkit))

<br >

.center[You can follow the story here: [GitHub Gist - Xavier basecalling notes](https://gist.github.com/sirselim/2ebe2807112fae93809aa18f096dbb94)]

---

# ~~The future...~~

.center[
<img src="images/jetson_family.jpg" style="width: 45%; margin-right: 1%; margin-top: 0em;"/>
]

.center[
<img src="images/nvidia_tegra.jpg" style="width: 40%; margin-right: 1%; margin-top: 0em;"/>
]

---

# ~~The (not so distant) future...~~

.center[
<img src="images/nvidia_tegra.jpg" style="width: 40%; margin-right: 1%; margin-top: 1.65em;"/>
]

---
class: hide_logo

# The present!

---
class: hide_logo

# The present!

---
class: hide_logo

# The present!

Can you sequence SARS-Cov2 on ~$100 USD compute? ... **YES!**

---
layout: false
class: hide_logo

---

# Hot off the press!

.center[
<img src="images/adaptive_sampling.jpeg" style="width: 85%; margin-right: 1%; margin-top: 1.65em;"/>
<br />
&copy; Oxford Nanopore Technologies
]
.center[
<br />
Jürgen Hench, Basel, Switzerland ([cancer methylation sequencing](https://gist.github.com/sirselim/2ebe2807112fae93809aa18f096dbb94#gistcomment-3547889))
]

---

# Hot off the press!

.center[
<img src="https://i.imgur.com/lhVYBf0.png" style="width: 65%; margin-right: 1%; margin-top: 1.65em;"/>
<br>
[Data generated a few hours ago... (excuse the mess!)](https://hackmd.io/_fMMOiDvRRiZ1f0cS0uchg?view)
]

---

# Hot off the press!

<article class="cf">
  <div class="fl w-50 bg-white tc">
    <img src="images/xavnx_phone.png" style="width: 45%; margin-right: 1%; margin-top: 0.5em;"/>
  </div>
  <div class="fl w-50 bg-white tc">
    <img src="images/minknowui.jpg" style="width: 97%; margin-right: 1%; margin-top: 0.5em;"/>
    <br>
    <br>
    <br>
    <br>
    <br>
    <b>Can now control all of this from our pockets!</b>  
    <br>
    <br>
    Available now on <a href="https://play.google.com/store/apps/details?id=com.nanoporetech.minknowui&hl=en_CA&gl=US" target="blank">Android</a> and <a href="https://apps.apple.com/us/app/minknow/id1504645283" target="blank">iOS</a>
  </div>
</article>

---

## Our experiences with the Jeston Xaviers

.small[
#### Article in the NZ Herald
  * The Genius of Genomics ([link](https://www.nzherald.co.nz/nz/the-genius-of-genomics-the-revolution-that-helped-nz-quash-covid-19/EFJWSHSL3TTYNNKYA5WEROIKHY/))
  * Story also on ESR website ([link](https://www.esr.cri.nz/home/about-esr/media-releases/esr-scientists-showcase-benefits-of-collaboration-for-rapid-dna-sequencing/))

#### Jetson Nanopore Sequencing 
  * [A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology](https://github.com/sirselim/jetson_nanopore_sequencing)
    * up to date information, including parts list and set up guide

<br>

#### Xavier AGX setup and notes
  * [Xavier AGX unboxing and setup](https://hackmd.io/@Miles/HkumH7sBH)

#### Xavier base-calling benchmarking and notes
  * [Xavier benchmarking](https://gist.github.com/sirselim/2ebe2807112fae93809aa18f096dbb94#file-basecalling_notes-md)
]

---

## Our experiences with the Jeston Xaviers

* [GPU musings (with an eye on genomics)](https://hackmd.io/@Miles/B1U-cOMyu)
  * [Setting up live GPU basecalling on Linux](https://github.com/sirselim/jetson_nanopore_sequencing/blob/main/live_basecalling.md)

<br>

#### Presentations

##### **eResearch 2020 presentation**

* [Assessing the potential of ~~autonomous AI devices~~ cool tech for portable real-time sequencing](https://sirselim.github.io/presentations/eResearch_2020/eResearch_presentation_livedemo_2020#1)
    * live base-calling and presentation run from the Xavier

##### **eResearch 2021 presentation**

* [Harnessing the disruptive nature of portable sequencing for community empowerment](https://sirselim.github.io/eResearch-Presentation-2021/index.html)
    * live sequencing and presentation run from the Xavier NX (SARS-COV2 sequencing)

##### **Nvidia Spring GPU Technology Conference 2021**

* [The disruptive nature of portable sequencing](https://sirselim.github.io/NvidiaGTC_2021/)
]

---

# If you're interested in GPUs and genomics...

.center[
<img src="images/gpu_musing_tweet.png" style="width: 45%; margin-right: 1%; margin-top: 1.65em;"/>
<br />
[GPU musings (with an eye on genomics)](https://hackmd.io/@Miles/B1U-cOMyu)
]

---
class: middle hide_logo

.center[
<img src="images/gtc21_mbenton.jpg" style="width: 90%; margin-right: 1%; margin-top: 1.65em;"/>
]

---
class: middle hide_logo

# Some parting thoughts

---

# acknowledgements (people to 'nerd' out with!)

<div class="dt dt--fixed">
  <div class="dtc tc pv4 bg-white">
    <article class="mw5 center bg-white br3 pa3 pa4-ns mv3 ba b--black-10">
      <div class="tc">
        <img src="images/Matt_sm.png" class="br-100 h4 w4 dib ba b--black-05 pa2" title="Photo of team member">
        <h4 class="f3 mb2">Matt Storey</h4>
        <h4 class="f5 fw4 gray mt0">(ESR)</h4>
      </div>
    </article>
  </div>
  <div class="dtc tc pv4 bg-white">
    <article class="mw5 center bg-white br3 pa3 pa4-ns mv3 ba b--black-10">
      <div class="tc">
        <img src="images/Joep.jpg" class="br-100 h4 w4 dib ba b--black-05 pa2" title="Photo of team member">
        <h4 class="f3 mb2">Joep de Ligt</h4>
        <h4 class="f5 fw4 gray mt0">(ESR)</h4>
      </div>
    </article>
  </div>
  <div class="dtc tc pv4 bg-white">
    <article class="mw5 center bg-white br3 pa3 pa4-ns mv3 ba b--black-10">
      <div class="tc">
        <img src="images/Donia.png" class="br-100 h4 w4 dib ba b--black-05 pa2" title="Photo of team member">
        <h4 class="f3 mb2">Donia Macartney-Coxson</h4>
        <h4 class="f5 fw4 gray mt0">(ESR)</h4>
      </div>
    </article>
  </div>
</div>

---
layout: false
class: hide_logo

Notes for current slide

Notes for next slide

The disruptive nature of portable sequencing for community empowerment… and GPUs

Genomics Aotearoa Friday Seminar Series, 9^th April 2021

Dr Miles Benton

Human Genomics
Institute of Environmental Science and Research (ESR)
Aotearoa (New Zealand)

1 / 53

Advocates for reproducible research...

Where possible all presentations and code are available online

sirselim.github.io/presentations

2 / 53

3 / 53

Who are we?

You may have seen recently...

4 / 53

Genomics in NZ's pandemic response

A sequencing success story made possible by the awesome Una Ren, Matt Storey & Joep de Ligt

Give us some time and money and we'll demonstrate what this technology can do.

5 / 53

Genomic sequencing

6 / 53

DNA - A, T, C, G Part of all 'living' things

A snapshot of the Human Genomics group

Independent research
- type-2 diabetes & obesity (genomics, epigenetics, protein 'omics)
- Guinea pigs! (Max Berry, University of Otago)
- empowering people to explore and interpret their data

Clinical diagnostics through genetics
- Contract(s) with CCDHB Wellington Regional Genetics Lab
- Providing support to CCDHB for Clinical Genomics GA project (Stephen Robertson)

Clinical research, in collaboration with local clinician (Richard Carroll) - hyperparathyroidism
- sequencing 100 exomes
- engaging clinicians from other DHBs
- exploring the replacement of gene panels with exome/genome

7 / 53

A big part of what we do is sequencing

8 / 53

(image source: illumina.com)

9 / 53

I used the word portable in my previous slide, this is not a phrase one would attribute to machines from Illumina / PacBio.

These things are huge! ... and expensive.

"Soon, It Will Cost Less To Sequence A Genome Than To Flush A Toilet -- And That Will Change Medicine Forever"

(image source: https://www.businessinsider.com.au/super-cheap-genome-sequencing)

10 / 53

Can we speed things up?

Thanks to eResearch 2020 ...enter Nvidia Clara Parabricks

powered by GPU

11 / 53

www.nvidia.com/en-us/healthcare/clara-parabricks/

12 / 53

How much does that matter?

Identical pipelines with a slight difference...

Pipeline [CPU]

Exomes: >100X exome takes between 8-12 hours
Genomes: ~30X genome takes between 30-48 hours

Pipeline [GPU - Parabricks]

Exomes: >100X exome takes between 6-12 mins
Genomes: 100X genome takes ~4 hours

was on 2x V100 GPUs, now also have 2x A100s

13 / 53

www.nvidia.com/en-us/healthcare/clara-parabricks/

14 / 53

15 / 53

Fun with Nvidia A100s!!

16 / 53

Complete Overhaul! [Leah Kemp]

Alignment and Variant Calling Workflow

[human_genomics_pipeline]

Variant Annotation Workflow

[annotation_pipeline]

Leah Kemp

(ESR)

ESR GitHub: https://github.com/ESR-NZ

17 / 53

Another type of sequencing technology

...sorry PacBio I'm ignoring you today...

18 / 53

(image source: nanoporetech)

19 / 53

flongle: ~$500 USD for 5 1 might be enough for a metagenome

minION: $1000

smidgION: still just a concept

gridION: ~$50K

promethION: ~$230K

slide kindly supplied by David Eccles (f1000 presentation) "Sequencing DNA with Linux Cores and Nanopores"

20 / 53

David's talk and a live demo are linked.

© Oxford Nanopore Technologies
21 / 53

Example squiggle plot

(image source: tombo manual)

22 / 53

What we 'see' when DNA passes through the pores.

GPUs accelerate basecalling of Nanopore long-read data (a lot)

Nanopore basecalling benchmarking: link (ESR GitHub)

23 / 53

Why GPUs?

New type of sequencing data requires new type of 'analysis'

squiggle data lends itself nicely to neural nets
GPUs are very capable in this space
- CUDA cores

ESR GPU basecalling benchmarks (link)

Titan RTX & 2x Tesla V100

Titan RTX

[UPDATE:] guppy is now able to scale across multiple GPUs!

24 / 53

Let's step back a couple of years

... a personal story ...

25 / 53

26 / 53

a personal story

had a lumbar puncture ('9 days' old)
- (after being born 8 weeks early)

suspected meningitis (bacteria/viral)?
- told after the fact

>48 hours for results return

27 / 53

a personal story

... imagine a more ‘real-time’ procedure:

28 / 53

a personal story

... imagine a more ‘real-time’ procedure:

a sample (i.e. blood) taken,
DNA/RNA extracted/enriched,
sequencing library prepared,
nanopore sequencing initiated,
sequence starts coming in almost instantly,
time to first read-match detection <1 hr

28 / 53

a personal story

... imagine a more ‘real-time’ procedure:

a sample (i.e. blood) taken,
DNA/RNA extracted/enriched,
sequencing library prepared,
nanopore sequencing initiated,
sequence starts coming in almost instantly,
time to first read-match detection <1 hr

This isn't a stretch of the imagination anymore, soon to be reality

28 / 53

Stress how fast and low cost this has the potential to be.

what are we doing?

Portable ‘real-time’ sequencing for the masses?

29 / 53

what are we doing?

Portable ‘real-time’ sequencing for the masses?

the idea
- low cost (< many mobile phones)
- accessible
- portable
- robust (...may have "performed" a drop test...)
- fun!

29 / 53

what are we doing?

Portable ‘real-time’ sequencing for the masses?

the idea
- low cost (< many mobile phones)
- accessible
- portable
- robust (...may have "performed" a drop test...)
- fun!
example use cases
- field sequencing (real-time monitoring, forensics, agriculture, waterways, ...)
- clinical settings
- community outreach / teaching

29 / 53

what are we doing?

Portable ‘real-time’ sequencing for the masses?

the idea
- low cost (< many mobile phones)
- accessible
- portable
- robust (...may have "performed" a drop test...)
- fun!
example use cases
- field sequencing (real-time monitoring, forensics, agriculture, waterways, ...)
- clinical settings
- community outreach / teaching

Community Science | "United in Data"

29 / 53

Our experiences with the Xavier (link)

30 / 53

Talk about the Xavier specs:

8 core arm
16 GB of RAM
512 CUDA core and 64 tensor cores
512 GB SSD NVMe

Benchmarking (link)^*

* spoilers for those following along live

31 / 53

Benchmarking (link)^*

* spoilers for those following along live

Most Jetson devices have the ability to be put into different power modes

Power.mode	Time
10W	33.4 mins
15W	14.3 mins
30W 2 cores	10.8 mins
30W 4 cores	10.8 mins
30W MAX (8 cores)	7.5 mins

Note: this table represents basecalling performed when running on a portable powerbank.

31 / 53

Why is 10W mode exciting?

We're running in 30W MAX mode for this live demo - running on a portable powerpack.

Very rough comparison of Nvidia ecosystem^#

Card	TFLOPS	Price	Power
Jetson Nano	~0.5	$99	5-10W
Jetson Xavier NX*	6	$399	10-15W
Jetson Xavier	11	$699	10-30W
Geforce 1080 Ti	11.3	~$650	215W
Geforce 2080 Ti	~13-14	~$800-$1000	250W
Titan RTX	16.3	~$3000	280W
Tesla V100	16.4	~$8500	250W

Price in USD
^# a very small selection of what Nvidia offers obviously!
* this can fit in an existing Jetson Nano carrier boards

32 / 53

V100 could rip through this data in a couple of mins, but consider the cost, power, etc.

Xavier NX is exciting, module that can slot into the Nano body [hold up Nano device]

Community engagement leading to empowerment

... a few stories of the journey ...

33 / 53

So how about unlocking it for everyone?

34 / 53

The unboxing and a slight snag

35 / 53

Success

36 / 53

A global cast of many

[Kenya] Jean-Bakka Domelevo Entfellner (@JeanBakaDE)
[USA] John Erb-Downward (@Bombanat)
[Italy] Luigi Faino (@lfaino)
[Switzerland] Jürgen Hench
[USA] Nvidia Clara Team (Clara AGX site)

You can follow the story here: GitHub Gist - Xavier basecalling notes

37 / 53

The future...

38 / 53

The (not so distant) future...

39 / 53

The present!

40 / 53

The present!

41 / 53

The present!

Can you sequence SARS-Cov2 on ~$100 USD compute? ... YES!

42 / 53

43 / 53

Hot off the press!

Jürgen Hench, Basel, Switzerland (cancer methylation sequencing)

44 / 53

Hot off the press!

Data generated a few hours ago... (excuse the mess!)

45 / 53

Hot off the press!

Can now control all of this from our pockets!

Available now on Android and iOS

46 / 53

Our experiences with the Jeston Xaviers

Article in the NZ Herald

The Genius of Genomics (link)
Story also on ESR website (link)

47 / 53

Our experiences with the Jeston Xaviers

Documentation

Presentations

eResearch 2020 presentation

Assessing the potential of ~~autonomous AI devices~~ cool tech for portable real-time sequencing
- live base-calling and presentation run from the Xavier

eResearch 2021 presentation

Harnessing the disruptive nature of portable sequencing for community empowerment
- live sequencing and presentation run from the Xavier NX (SARS-COV2 sequencing)

Nvidia Spring GPU Technology Conference 2021

The disruptive nature of portable sequencing

48 / 53

If you're interested in GPUs and genomics...

GPU musings (with an eye on genomics)

49 / 53

50 / 53

Some parting thoughts51 / 53

acknowledgements (people to 'nerd' out with!)

Matt Storey

(ESR)

Joep de Ligt

(ESR)

Donia Macartney-Coxson

(ESR)

Georgia Bell (ESR)
Una Ren (ESR)
Leah Kemp (ESR)

Matthew Walton (ESR)
Richard Dean (ESR)
Russell Smithies (ESR)

52 / 53

53 / 53

Advocates for reproducible research...

Where possible all presentations and code are available online

sirselim.github.io/presentations

2 / 53

Paused

Help

Keyboard shortcuts

↑, ←, Pg Up, k	Go to previous slide
↓, →, Pg Dn, Space, j	Go to next slide
Home	Go to first slide
End	Go to last slide
Number + Return	Go to specific slide
b / m / f	Toggle blackout / mirrored / fullscreen mode
c	Clone slideshow
p	Toggle presenter mode
t	Restart the presentation timer
?, h	Toggle this help
o	Tile View: Overview of Slides

Esc	Back to slideshow

The disruptive nature of portable sequencing for community empowerment… and GPUs

Genomics Aotearoa Friday Seminar Series, 9^th April 2021

Dr Miles Benton

Human Genomics
Institute of Environmental Science and Research (ESR)
Aotearoa (New Zealand)

1 / 53

Advocates for reproducible research...

Where possible all presentations and code are available online

sirselim.github.io/presentations

2 / 53

3 / 53

Who are we?

You may have seen recently...

4 / 53

Genomics in NZ's pandemic response

A sequencing success story made possible by the awesome Una Ren, Matt Storey & Joep de Ligt

Give us some time and money and we'll demonstrate what this technology can do.

5 / 53

Genomic sequencing

6 / 53

DNA - A, T, C, G Part of all 'living' things

A snapshot of the Human Genomics group

Independent research
- type-2 diabetes & obesity (genomics, epigenetics, protein 'omics)
- Guinea pigs! (Max Berry, University of Otago)
- empowering people to explore and interpret their data

Clinical diagnostics through genetics
- Contract(s) with CCDHB Wellington Regional Genetics Lab
- Providing support to CCDHB for Clinical Genomics GA project (Stephen Robertson)

Clinical research, in collaboration with local clinician (Richard Carroll) - hyperparathyroidism
- sequencing 100 exomes
- engaging clinicians from other DHBs
- exploring the replacement of gene panels with exome/genome

7 / 53

A big part of what we do is sequencing

8 / 53

(image source: illumina.com)

9 / 53

I used the word portable in my previous slide, this is not a phrase one would attribute to machines from Illumina / PacBio.

These things are huge! ... and expensive.

"Soon, It Will Cost Less To Sequence A Genome Than To Flush A Toilet -- And That Will Change Medicine Forever"

(image source: https://www.businessinsider.com.au/super-cheap-genome-sequencing)

10 / 53

Can we speed things up?

Thanks to eResearch 2020 ...enter Nvidia Clara Parabricks

powered by GPU

11 / 53

www.nvidia.com/en-us/healthcare/clara-parabricks/

12 / 53

How much does that matter?

Identical pipelines with a slight difference...

Pipeline [CPU]

Exomes: >100X exome takes between 8-12 hours
Genomes: ~30X genome takes between 30-48 hours

Pipeline [GPU - Parabricks]

Exomes: >100X exome takes between 6-12 mins
Genomes: 100X genome takes ~4 hours

was on 2x V100 GPUs, now also have 2x A100s

13 / 53

www.nvidia.com/en-us/healthcare/clara-parabricks/

14 / 53

15 / 53

Fun with Nvidia A100s!!

16 / 53

Complete Overhaul! [Leah Kemp]

Alignment and Variant Calling Workflow

[human_genomics_pipeline]

Variant Annotation Workflow

[annotation_pipeline]

Leah Kemp

(ESR)

ESR GitHub: https://github.com/ESR-NZ

17 / 53

Another type of sequencing technology

...sorry PacBio I'm ignoring you today...

18 / 53

(image source: nanoporetech)

19 / 53

flongle: ~$500 USD for 5 1 might be enough for a metagenome

minION: $1000

smidgION: still just a concept

gridION: ~$50K

promethION: ~$230K

slide kindly supplied by David Eccles (f1000 presentation) "Sequencing DNA with Linux Cores and Nanopores"

20 / 53

David's talk and a live demo are linked.

© Oxford Nanopore Technologies
21 / 53

Example squiggle plot

(image source: tombo manual)

22 / 53

What we 'see' when DNA passes through the pores.

GPUs accelerate basecalling of Nanopore long-read data (a lot)

Nanopore basecalling benchmarking: link (ESR GitHub)

23 / 53

Why GPUs?

New type of sequencing data requires new type of 'analysis'

squiggle data lends itself nicely to neural nets
GPUs are very capable in this space
- CUDA cores

ESR GPU basecalling benchmarks (link)

Titan RTX & 2x Tesla V100

Titan RTX

[UPDATE:] guppy is now able to scale across multiple GPUs!

24 / 53

Let's step back a couple of years

... a personal story ...

25 / 53

26 / 53

a personal story

had a lumbar puncture ('9 days' old)
- (after being born 8 weeks early)

suspected meningitis (bacteria/viral)?
- told after the fact

>48 hours for results return

27 / 53

a personal story

... imagine a more ‘real-time’ procedure:

28 / 53

a personal story

... imagine a more ‘real-time’ procedure:

a sample (i.e. blood) taken,
DNA/RNA extracted/enriched,
sequencing library prepared,
nanopore sequencing initiated,
sequence starts coming in almost instantly,
time to first read-match detection <1 hr

28 / 53

a personal story

... imagine a more ‘real-time’ procedure:

a sample (i.e. blood) taken,
DNA/RNA extracted/enriched,
sequencing library prepared,
nanopore sequencing initiated,
sequence starts coming in almost instantly,
time to first read-match detection <1 hr

This isn't a stretch of the imagination anymore, soon to be reality

28 / 53

Stress how fast and low cost this has the potential to be.

what are we doing?

Portable ‘real-time’ sequencing for the masses?

29 / 53

what are we doing?

Portable ‘real-time’ sequencing for the masses?

the idea
- low cost (< many mobile phones)
- accessible
- portable
- robust (...may have "performed" a drop test...)
- fun!

29 / 53

what are we doing?

Portable ‘real-time’ sequencing for the masses?

the idea
- low cost (< many mobile phones)
- accessible
- portable
- robust (...may have "performed" a drop test...)
- fun!
example use cases
- field sequencing (real-time monitoring, forensics, agriculture, waterways, ...)
- clinical settings
- community outreach / teaching

29 / 53

what are we doing?

Portable ‘real-time’ sequencing for the masses?

the idea
- low cost (< many mobile phones)
- accessible
- portable
- robust (...may have "performed" a drop test...)
- fun!
example use cases
- field sequencing (real-time monitoring, forensics, agriculture, waterways, ...)
- clinical settings
- community outreach / teaching

Community Science | "United in Data"

29 / 53

Our experiences with the Xavier (link)

30 / 53

Talk about the Xavier specs:

8 core arm
16 GB of RAM
512 CUDA core and 64 tensor cores
512 GB SSD NVMe

Benchmarking (link)^*

* spoilers for those following along live

31 / 53

Benchmarking (link)^*

* spoilers for those following along live

Most Jetson devices have the ability to be put into different power modes

Note: this table represents basecalling performed when running on a portable powerbank.

31 / 53

Why is 10W mode exciting?

We're running in 30W MAX mode for this live demo - running on a portable powerpack.

Very rough comparison of Nvidia ecosystem^#

Price in USD
^# a very small selection of what Nvidia offers obviously!
* this can fit in an existing Jetson Nano carrier boards

32 / 53

V100 could rip through this data in a couple of mins, but consider the cost, power, etc.

Xavier NX is exciting, module that can slot into the Nano body [hold up Nano device]

Community engagement leading to empowerment

... a few stories of the journey ...

33 / 53

So how about unlocking it for everyone?

34 / 53

The unboxing and a slight snag

35 / 53

Success

36 / 53

A global cast of many

[Kenya] Jean-Bakka Domelevo Entfellner (@JeanBakaDE)
[USA] John Erb-Downward (@Bombanat)
[Italy] Luigi Faino (@lfaino)
[Switzerland] Jürgen Hench
[USA] Nvidia Clara Team (Clara AGX site)

You can follow the story here: GitHub Gist - Xavier basecalling notes

37 / 53

The future...

38 / 53

The (not so distant) future...

39 / 53

The present!

40 / 53

The present!

41 / 53

The present!

Can you sequence SARS-Cov2 on ~$100 USD compute? ... YES!

42 / 53

43 / 53

Hot off the press!

Jürgen Hench, Basel, Switzerland (cancer methylation sequencing)

44 / 53

Hot off the press!

Data generated a few hours ago... (excuse the mess!)

45 / 53

Hot off the press!

Can now control all of this from our pockets!

Available now on Android and iOS

46 / 53

Our experiences with the Jeston Xaviers

Article in the NZ Herald

The Genius of Genomics (link)
Story also on ESR website (link)

Jetson Nanopore Sequencing

A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology
- up to date information, including parts list and set up guide

Xavier AGX setup and notes

Xavier AGX unboxing and setup

Xavier base-calling benchmarking and notes

Xavier benchmarking

47 / 53

Our experiences with the Jeston Xaviers

Documentation

Presentations

eResearch 2020 presentation

Assessing the potential of ~~autonomous AI devices~~ cool tech for portable real-time sequencing
- live base-calling and presentation run from the Xavier

eResearch 2021 presentation

Harnessing the disruptive nature of portable sequencing for community empowerment
- live sequencing and presentation run from the Xavier NX (SARS-COV2 sequencing)

Nvidia Spring GPU Technology Conference 2021

The disruptive nature of portable sequencing

48 / 53

If you're interested in GPUs and genomics...

GPU musings (with an eye on genomics)

49 / 53

50 / 53

Some parting thoughts51 / 53

acknowledgements (people to 'nerd' out with!)

Matt Storey

(ESR)

Joep de Ligt

(ESR)

Donia Macartney-Coxson

(ESR)

Georgia Bell (ESR)
Una Ren (ESR)
Leah Kemp (ESR)

Matthew Walton (ESR)
Richard Dean (ESR)
Russell Smithies (ESR)

52 / 53

53 / 53

The disruptive nature of portable sequencing for community empowerment… and GPUs

Genomics Aotearoa Friday Seminar Series, 9th April 2021

Advocates for reproducible research...

Where possible all presentations and code are available online

Who are we?

Genomics in NZ's pandemic response

A sequencing success story made possible by the awesome Una Ren, Matt Storey & Joep de Ligt

A snapshot of the Human Genomics group

A big part of what we do is sequencing

Can we speed things up?

How much does that matter?

Identical pipelines with a slight difference...

Complete Overhaul! [Leah Kemp]

Leah Kemp

(ESR)

Another type of sequencing technology

Example squiggle plot

GPUs accelerate basecalling of Nanopore long-read data (a lot)

Why GPUs?

Let's step back a couple of years

a personal story

a personal story

a personal story

a personal story

what are we doing?

what are we doing?

what are we doing?

what are we doing?

Our experiences with the Xavier (link)

Benchmarking (link)*

Benchmarking (link)*

Very rough comparison of Nvidia ecosystem#

Community engagement leading to empowerment

So how about unlocking it for everyone?

The unboxing and a slight snag

Success

A global cast of many

The future...

The (not so distant) future...

The present!

The present!

The present!

Hot off the press!

Hot off the press!

Hot off the press!

Our experiences with the Jeston Xaviers

Article in the NZ Herald

Jetson Nanopore Sequencing

Xavier AGX setup and notes

Xavier base-calling benchmarking and notes

Our experiences with the Jeston Xaviers

Documentation

Presentations

eResearch 2020 presentation

eResearch 2021 presentation

Nvidia Spring GPU Technology Conference 2021

If you're interested in GPUs and genomics...

Some parting thoughts

acknowledgements (people to 'nerd' out with!)

Matt Storey

(ESR)

Joep de Ligt

(ESR)

Donia Macartney-Coxson

(ESR)

Advocates for reproducible research...

Where possible all presentations and code are available online

Help

.large[The disruptive nature of portable sequencing for community empowerment… and GPUs]

The disruptive nature of portable sequencing for community empowerment… and GPUs

Genomics Aotearoa Friday Seminar Series, 9th April 2021

Advocates for reproducible research...

Where possible all presentations and code are available online

Who are we?

Genomics in NZ's pandemic response

A sequencing success story made possible by the awesome Una Ren, Matt Storey & Joep de Ligt

A snapshot of the Human Genomics group

A big part of what we do is sequencing

Can we speed things up?

How much does that matter?

Genomics Aotearoa Friday Seminar Series, 9^th April 2021

Benchmarking (link)^*

Benchmarking (link)^*

Very rough comparison of Nvidia ecosystem^#

Genomics Aotearoa Friday Seminar Series, 9^th April 2021

Benchmarking (link)^*

Benchmarking (link)^*

Very rough comparison of Nvidia ecosystem^#