The Genome Assembly Problem

•

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a lightning talk about the de Bruijn Graphs assembling algorithm

The Genome Assembly
Problem
a lightning talk
Mark Chang

The Genome Assembly Problem
ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT
ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT
Fragmented and Sequenced
Finding Overlaps
Recunstruction
CGTAGCGTTTGTGGGTACCTCAGAACCC
AACCCCGCAGTCACGTAG GTGGGTACCTCGTG
TCGTGTCTAGT
Genome
ACCTCAGAACCC
AACCCCGCAGTCACGTAG
GTGGGTACCTCGTGCGTAGCGTTTGTGGGT
TCGTGTCTAGT
Short-reads

Finding Overlaps
• It is very hard to find the overlaps between millions of short-reads
ACCTCAGAACCC
AACCCCGCAGTCACGTAG
GTGGGTACCTCGTGCGTAGCGTTTGTGGGT
TCGTGTCTAGT

Finding Overlaps
• Using de Bruijn Graphs
AAB
CDC
ABC
BCC
CCD
CDA
DCC
AABCCDCCDA
graph traversal
AABCCDCCDA
convert to de Bruijn Graph

Using de Bruijn Graphs
• Convert the short-reads into k-mers
ACCTCAGAACCC AACCCCGCAGTCACGTAG
GAACC
AGAAC
CAGAA
ACCTC
CCTCA
CTCAG
TCAGA
AACCC
AACCC
ACGTA
CACGT
GCAGT
CGCAG
CCGCA
CCCGC
ACCCC
CCCCG
CGTAG

Using de Bruijn Graphs
• Build de bruijn graph from k-mers
GAACC
AGAAC
CAGAA
ACCTC
CCTCA
CTCAG
TCAGA
AACCC
GAACC AGAAC CAGAA
ACCTC CCTCA CTCAG TCAGA
AACCC

Using de Bruijn Graphs
• Build de bruijn graph from k-mers
GAACC AGAAC CAGAA
ACCTC CCTCA CTCAG TCAGA
AACCC
AACCC
ACGTA
CACGT
GCAGT
CGCAG
CCGCA
CCCGC
ACCCC
CCCCG
CGTAG
ACGTA CACGT GCAGT CGCAG
CCGCACCCGCACCCC CCCCG
CGTAG

Using de Bruijn Graphs
• Graph traversal
ACCTCAGAACCCCGCAGTCACGTAG
GAACC AGAAC CAGAA
ACCTC CCTCA CTCAG TCAGA
AACCC
ACGTA CACGT GCAGT CGCAG
CCGCACCCGCACCCC CCCCG
CGTAG

Reference
• The Genome Assembly Problem
• http://homolog.us/Tutorials/index.php?p=1.1&s=1

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ScienceShare.co.uk Shared Resource

Ashg2017 workshop tg

Ashg2017 workshop tg

Ashg2017 workshop tg

PLC

More from Mark Chang

Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Information in the Weights

Information in the Weights

Information in the Weights

Information in the Weights

Information in the Weights

Information in the Weights

PAC Bayesian for Deep Learning

PAC Bayesian for Deep Learning

PAC Bayesian for Deep Learning

PAC-Bayesian Bound for Deep Learning

PAC-Bayesian Bound for Deep Learning

PAC-Bayesian Bound for Deep Learning

Domain Adaptation

Domain Adaptation

Domain Adaptation

NTU ML TENSORFLOW

NTU ML TENSORFLOW

NTU ML TENSORFLOW

Applied Deep Learning 11/03 Convolutional Neural Networks

Applied Deep Learning 11/03 Convolutional Neural Networks

Applied Deep Learning 11/03 Convolutional Neural Networks

淺談深度學習

Variational Autoencoder

Variational Autoencoder

Variational Autoencoder

TensorFlow 深度學習快速上手班--深度學習

TensorFlow 深度學習快速上手班--深度學習

TensorFlow 深度學習快速上手班--深度學習

TensorFlow 深度學習快速上手班--自然語言處理應用

TensorFlow 深度學習快速上手班--自然語言處理應用

TensorFlow 深度學習快速上手班--自然語言處理應用

TensorFlow 深度學習快速上手班--機器學習

TensorFlow 深度學習快速上手班--機器學習

TensorFlow 深度學習快速上手班--機器學習

Computational Linguistics week 10

Computational Linguistics week 10

Computational Linguistics week 10

Neural Doodle

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TensorFlow 深度學習講座

TensorFlow 深度學習講座

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Computational Linguistics week 5

Computational Linguistics week 5

Neural Art (English Version)

Neural Art (English Version)

Neural Art (English Version)

AlphaGo in Depth

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Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Modeling the Dynamics of SGD by Stochastic Differential Equation

Information in the Weights

Information in the Weights

Information in the Weights

Information in the Weights

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Information in the Weights

PAC Bayesian for Deep Learning

PAC Bayesian for Deep Learning

PAC Bayesian for Deep Learning

PAC-Bayesian Bound for Deep Learning

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NTU ML TENSORFLOW

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Applied Deep Learning 11/03 Convolutional Neural Networks

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Variational Autoencoder

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Increase engagement and revenue with Muvi Live Paywall! In this presentation, we will explore the five key benefits of using Muvi Live Paywall to monetize your live streams. You'll learn how Muvi Live Paywall can help you: Monetize your live content easily: Set up pay-per-view access to your live streams and start generating revenue from your content. Increase audience engagement: Provide exclusive, premium content behind the paywall to keep your viewers engaged. Gain valuable viewer insights: Track viewer data and analytics to better understand your audience and tailor your content accordingly. Reduce content piracy: Muvi Live Paywall's security features help protect your content from unauthorized distribution. Streamline your workflow: The all-in-one platform simplifies the process of managing and monetizing your live streams. With Muvi Live Paywall, you can take control of your live stream monetization and create a sustainable business model for your content. Learn more about Muvi Live Paywall and start generating revenue from your live streams today!

Top 5 Benefits OF Using Muvi Live Paywall For Live Streams

Top 5 Benefits OF Using Muvi Live Paywall For Live Streams

Top 5 Benefits OF Using Muvi Live Paywall For Live Streams

Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving

Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving

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Boost Fertility New Invention Ups Success Rates.pdf

Boost Fertility New Invention Ups Success Rates.pdf

Boost Fertility New Invention Ups Success Rates.pdf

sudhanshuwaghmare1

Abhishek Deb(1), Mr Abdul Kalam(2) M. Des (UX) , School of Design, DIT University , Dehradun. This paper explores the future potential of AI-enabled smartphone processors, aiming to investigate the advancements, capabilities, and implications of integrating artificial intelligence (AI) into smartphone technology. The research study goals consist of evaluating the development of AI in mobile phone processors, analyzing the existing state as well as abilities of AI-enabled cpus determining future patterns as well as chances together with reviewing obstacles as well as factors to consider for more growth.

Exploring the Future Potential of AI-Enabled Smartphone Processors

Exploring the Future Potential of AI-Enabled Smartphone Processors

Exploring the Future Potential of AI-Enabled Smartphone Processors

MySQL Webinar, presented on the 25th of April, 2024. Summary: MySQL solutions enable the deployment of diverse Database Architectures tailored to specific needs, including High Availability, Disaster Recovery, and Read Scale-Out. With MySQL Shell's AdminAPI, administrators can seamlessly set up, manage, and monitor these solutions, ensuring efficiency and ease of use in their administration. MySQL Router, on the other hand, provides transparent routing from the application traffic to the backend servers in the architectures, requiring minimal configuration. Completely built in-house and supported by Oracle, these solutions have been adopted by enterprises of all sizes for their business-critical applications. In this presentation, we'll delve into various database architecture solutions to help you choose the right one based on your business requirements. Focusing on technical details and the latest features to maximize the potential of these solutions.

Mastering MySQL Database Architecture: Deep Dive into MySQL Shell and MySQL R...

Mastering MySQL Database Architecture: Deep Dive into MySQL Shell and MySQL R...

Mastering MySQL Database Architecture: Deep Dive into MySQL Shell and MySQL R...

The Good, the Bad and the Governed - Why is governance a dirty word? David O'Neill, Chief Operating Officer - APIContext Apidays New York 2024: The API Economy in the AI Era (April 30 & May 1, 2024) ------ Check out our conferences at https://www.apidays.global/ Do you want to sponsor or talk at one of our conferences? https://apidays.typeform.com/to/ILJeAaV8 Learn more on APIscene, the global media made by the community for the community: https://www.apiscene.io Explore the API ecosystem with the API Landscape: https://apilandscape.apiscene.io/

Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...

Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...

Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...

With more memory available, system performance of three Dell devices increased, which can translate to a better user experience Conclusion When your system has plenty of RAM to meet your needs, you can efficiently access the applications and data you need to finish projects and to-do lists without sacrificing time and focus. Our test results show that with more memory available, three Dell PCs delivered better performance and took less time to complete the Procyon Office Productivity benchmark. These advantages translate to users being able to complete workflows more quickly and multitask more easily. Whether you need the mobility of the Latitude 5440, the creative capabilities of the Precision 3470, or the high performance of the OptiPlex Tower Plus 7010, configuring your system with more RAM can help keep processes running smoothly, enabling you to do more without compromising performance.

Boost PC performance: How more available memory can improve productivity

Boost PC performance: How more available memory can improve productivity

Boost PC performance: How more available memory can improve productivity

Principled Technologies

Polkadot JAM Slides - Token2049 - By Dr. Gavin Wood

Polkadot JAM Slides - Token2049 - By Dr. Gavin Wood

Polkadot JAM Slides - Token2049 - By Dr. Gavin Wood

Juan lago vázquez

Automating Google Workspace (GWS) & more with Apps Script

Automating Google Workspace (GWS) & more with Apps Script

Automating Google Workspace (GWS) & more with Apps Script

Join our latest Connector Corner webinar to discover how UiPath Integration Service revolutionizes API-centric automation in a 'Quote to Cash' process—and how that automation empowers businesses to accelerate revenue generation. A comprehensive demo will explore connecting systems, GenAI, and people, through powerful pre-built connectors designed to speed process cycle times. Speakers: James Dickson, Senior Software Engineer Charlie Greenberg, Host, Product Marketing Manager

Connector Corner: Accelerate revenue generation using UiPath API-centric busi...

Connector Corner: Accelerate revenue generation using UiPath API-centric busi...

Connector Corner: Accelerate revenue generation using UiPath API-centric busi...

This presentations targets students or working professionals. You may know Google for search, YouTube, Android, Chrome, and Gmail, but did you know Google has many developer tools, platforms & APIs? This comprehensive yet still high-level overview outlines the most impactful tools for where to run your code, store & analyze your data. It will also inspire you as to what's possible. This talk is 50 minutes in length.

Powerful Google developer tools for immediate impact! (2023-24 C)

Powerful Google developer tools for immediate impact! (2023-24 C)

Powerful Google developer tools for immediate impact! (2023-24 C)

Three things you will take away from the session: • How to run an effective tenant-to-tenant migration • Best practices for before, during, and after migration • Tips for using migration as a springboard to prepare for Copilot in Microsoft 365 Main ideas: Migration Overview: The presentation covers the current reality of cross-tenant migrations, the triggers, phases, best practices, and benefits of a successful tenant migration Considerations: When considering a migration, it is important to consider the migration scope, performance, customization, flexibility, user-friendly interface, automation, monitoring, support, training, scalability, data integrity, data security, cost, and licensing structure Next Wave: The next wave of change includes the launch of Copilot, which requires businesses to be prepared for upcoming changes related to Copilot and the cloud, and to consolidate data and tighten governance ShareGate: ShareGate can help with pre-migration analysis, configurable migration tool, and automated, end-user driven collaborative governance

Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff

Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff

Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff

A Domino Admins Adventures (Engage 2024)

A Domino Admins Adventures (Engage 2024)

A Domino Admins Adventures (Engage 2024)

Gabriella Davis

Partners Life - Insurer Innovation Award 2024

Partners Life - Insurer Innovation Award 2024

Partners Life - Insurer Innovation Award 2024

The Digital Insurer

ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke

ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke

ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke

Product Anonymous

Workshop - Best of Both Worlds_ Combine KG and Vector search for enhanced R...

Workshop - Best of Both Worlds_ Combine KG and Vector search for enhanced R...

Workshop - Best of Both Worlds_ Combine KG and Vector search for enhanced R...

GenAI Risks & Security Meetup 01052024.pdf

GenAI Risks & Security Meetup 01052024.pdf

GenAI Risks & Security Meetup 01052024.pdf

The 7 Things I Know About Cyber Security After 25 Years | April 2024

The 7 Things I Know About Cyber Security After 25 Years | April 2024

The 7 Things I Know About Cyber Security After 25 Years | April 2024

Effective data discovery is crucial for maintaining compliance and mitigating risks in today's rapidly evolving privacy landscape. However, traditional manual approaches often struggle to keep pace with the growing volume and complexity of data. Join us for an insightful webinar where industry leaders from TrustArc and Privya will share their expertise on leveraging AI-powered solutions to revolutionize data discovery. You'll learn how to: - Effortlessly maintain a comprehensive, up-to-date data inventory - Harness code scanning insights to gain complete visibility into data flows leveraging the advantages of code scanning over DB scanning - Simplify compliance by leveraging Privya's integration with TrustArc - Implement proven strategies to mitigate third-party risks Our panel of experts will discuss real-world case studies and share practical strategies for overcoming common data discovery challenges. They'll also explore the latest trends and innovations in AI-driven data management, and how these technologies can help organizations stay ahead of the curve in an ever-changing privacy landscape.

TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery

TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery

TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery

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Top 5 Benefits OF Using Muvi Live Paywall For Live Streams

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Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving

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Boost Fertility New Invention Ups Success Rates.pdf

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Exploring the Future Potential of AI-Enabled Smartphone Processors

Exploring the Future Potential of AI-Enabled Smartphone Processors

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Mastering MySQL Database Architecture: Deep Dive into MySQL Shell and MySQL R...

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Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...

Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...

Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...

Boost PC performance: How more available memory can improve productivity

Boost PC performance: How more available memory can improve productivity

Boost PC performance: How more available memory can improve productivity

Polkadot JAM Slides - Token2049 - By Dr. Gavin Wood

Polkadot JAM Slides - Token2049 - By Dr. Gavin Wood

Polkadot JAM Slides - Token2049 - By Dr. Gavin Wood

Automating Google Workspace (GWS) & more with Apps Script

Automating Google Workspace (GWS) & more with Apps Script

Automating Google Workspace (GWS) & more with Apps Script

Connector Corner: Accelerate revenue generation using UiPath API-centric busi...

Connector Corner: Accelerate revenue generation using UiPath API-centric busi...

Connector Corner: Accelerate revenue generation using UiPath API-centric busi...

Powerful Google developer tools for immediate impact! (2023-24 C)

Powerful Google developer tools for immediate impact! (2023-24 C)

Powerful Google developer tools for immediate impact! (2023-24 C)

Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff

Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff

Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff

A Domino Admins Adventures (Engage 2024)

A Domino Admins Adventures (Engage 2024)

A Domino Admins Adventures (Engage 2024)

Partners Life - Insurer Innovation Award 2024

Partners Life - Insurer Innovation Award 2024

Partners Life - Insurer Innovation Award 2024

ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke

ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke

ProductAnonymous-April2024-WinProductDiscovery-MelissaKlemke

Workshop - Best of Both Worlds_ Combine KG and Vector search for enhanced R...

Workshop - Best of Both Worlds_ Combine KG and Vector search for enhanced R...

Workshop - Best of Both Worlds_ Combine KG and Vector search for enhanced R...

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GenAI Risks & Security Meetup 01052024.pdf

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The 7 Things I Know About Cyber Security After 25 Years | April 2024

The 7 Things I Know About Cyber Security After 25 Years | April 2024

TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery

TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery

TrustArc Webinar - Unlock the Power of AI-Driven Data Discovery

The Genome Assembly Problem

1. The Genome Assembly Problem a lightning talk Mark Chang

2. The Genome Assembly Problem ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT Fragmented and Sequenced Finding Overlaps Recunstruction CGTAGCGTTTGTGGGTACCTCAGAACCC AACCCCGCAGTCACGTAG GTGGGTACCTCGTG TCGTGTCTAGT Genome ACCTCAGAACCC AACCCCGCAGTCACGTAG GTGGGTACCTCGTGCGTAGCGTTTGTGGGT TCGTGTCTAGT Short-reads

3. Finding Overlaps • It is very hard to find the overlaps between millions of short-reads ACCTCAGAACCC AACCCCGCAGTCACGTAG GTGGGTACCTCGTGCGTAGCGTTTGTGGGT TCGTGTCTAGT

4. Finding Overlaps • Using de Bruijn Graphs AAB CDC ABC BCC CCD CDA DCC AABCCDCCDA graph traversal AABCCDCCDA convert to de Bruijn Graph

5. Using de Bruijn Graphs • Convert the short-reads into k-mers ACCTCAGAACCC AACCCCGCAGTCACGTAG GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC AACCC ACGTA CACGT GCAGT CGCAG CCGCA CCCGC ACCCC CCCCG CGTAG

6. Using de Bruijn Graphs • Build de bruijn graph from k-mers GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC

7. Using de Bruijn Graphs • Build de bruijn graph from k-mers GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC AACCC ACGTA CACGT GCAGT CGCAG CCGCA CCCGC ACCCC CCCCG CGTAG ACGTA CACGT GCAGT CGCAG CCGCACCCGCACCCC CCCCG CGTAG

8. Using de Bruijn Graphs • Graph traversal ACCTCAGAACCCCGCAGTCACGTAG GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC ACGTA CACGT GCAGT CGCAG CCGCACCCGCACCCC CCCCG CGTAG

9. Reference • The Genome Assembly Problem • http://homolog.us/Tutorials/index.php?p=1.1&s=1