CLC bio presentation at 5th SFAF 6/3/2010

•Download as PPTX, PDF•

0 likes•794 views

My presentation at the 5th Sequencing FInishing and Analysis in the Future (SFAF -- http://www.lanl.gov/conferences/finishfuture/2010SFAF_Meeting_Guide.pdf) June 3, 2010

Technology Education

CLC bio A Comprehensive Platform for NGS Data Analysis Saul A. Kravitz, PhD Director of Consulting Services

Before the Flood 2005: $5M Human genome – 19 sequencer years Sample Prep Analysis Sequencing Science

Nextgen Sequencing Revolution 2010: $6k Human genome ~1 sequencer day Help!! Sample Prep Analysis Sequencing Science

Bioinformatics Challenges ,[object Object]

Rapid technology change, applications growth

Rapid customization and adaptation,[object Object]

Swiss Army Knife of NGS Analysis SDK Intuitive GUI Traditional Bioinformatics Visualization Desktop Solutions EnterpriseSolutions High Performance File Format Conversion Tools Integration Epigenomics Transcriptomics Genomics RNA-Seq miRNA Read Mapping De Novo Assembly SNP/DIP Detection CHIP-Seq

Why not use free tools? Are tools free or “free”? Tools vs solutions True cost of ownership Ease of Use Tools integration Support

Small RNA Analysis(in Beta soon) Identify and filter/trim adapters annotate using mirBASE and other resources - target species of interest Merge/group by mature, precursor/reference Fully integrated with expression analysis

De Novo Assembler Human assembly of 38x Illumina paired-end CLC Quality equivalent to Abyss CLC: 7 hrs, 1 node, 42 Gbof RAM Abyss: 80 hrs, 21 nodes, 336 Gbof RAM Metagenomics Assembly METAHIT Dataset MH0041 40M 75bp paired end 3 hrs on desktop, 6 Gb RAM Higher N50 and Total Contig Size than Reported

Sanger sequencing using fluorescent BigDye® terminator chemistry and semi‐automated capillary electrophoresis (CE) has long been considered the gold standard for identifying sequence variations such as disease‐causing mutations. The robustness, low error rate, ease of use, human interpretable visual displays of the signals generated by the instruments, and low cost per sample and target have all contributed to this reputation. Homozygous and heterozygous germ line mutations are reliably detected and reported using established DNA sequencing analysis software such as the Applied Biosystems Variant Reporter™ software. However, somatic variants with an allelic proportion of 25% or less are often undetected (i.e. not "called") by the software and thus escape awareness if not detected by careful visual inspection of the electropherograms. With the rapid adoption of next generation sequencing technology (NGS) and its use for characterization of specific and discrete mutations in tumor samples, an urgent need has emerged to establish an orthogonal technology for reliable and sensitive detection of somatic mutations which may occur at proportions of 10% or lower compared to the normal allele. To this end, we have developed an innovative algorithm, software, and a protocol that specialize in the detection and reporting of minor mutations by Sanger sequencing. Moreover the algorithm preserves the ability to generate the familiar displays of the data to facilitate human review. Using panels of prepared mixtures of minor alleles in the range of 2.5%, 5%, 10% and 20%, we have achieved 94.6% sensitivity and 99.8% specificity for automated detection of mutations present at the 5% level with high quality data. In conclusion, we have demonstrated that standard protocols for fluorescent dye terminator Sanger sequencing in conjunction with the new algorithm delivered in Variant Finder software may enable the identification of de novo somatic mutations to a level of 5%. This technology will also be useful for the confirmation of minor variants identified by NGS platforms.

Brendel Group Presentation: 5 Nov 2013

danielstandage

Next generation sequencing & microarray-- Genotypic Technology

Genotypic Technology

Greetings from Genotypic Technology, Bangalore (www.genotypic.co.in). We are a 13 year old genomics and bioinformatics company ( 65+ employees, Service. Products and R & D) based in Bangalore, India, primarily working on applications of Microarrays and Next Generation Sequencing in Human Health and Disease, including in Molecular Diagnostics, Prognosis, Therapeutics, Vaccine Research, Basic Science Research, Veterinary Science, Agriculture, Industrial Biotechnology, Microbial Genetics and more. Our major strength is in customized genomics solutions, particularly in your field, we can develop panel of markers for specific diseases, optimize, validate and help commercialize on open platforms or specific instrument platforms- in microarrays and sequencing based methods/ assays. We can also use genomic markers to aid in treatment of specific disease using personalized medicine approaches. All this can be done on a comprehensive end-to-end manner in our company as we have a very good blend of molecular biology and bioinformatics with totally 6 Ph.Ds. We work closely with Agilent's R &D as their partner.

Poster ESHGKirsten van Nimwegen

Ngs webinar 2013Elsa von Licy

Biz model for ion proton dna sequencer

Jeffrey Funk Business Models

my students use ideas from my class on business models to develop a business model for ion proton's DNA sequencer. This sequencer uses semiconductor technology to read an organism's DNA sequence and is faster and cheaper than existing sequencers. This presentation describes the value proposition, customer selection, method of value capture and other aspects of a business model for Ion Proton's DNA sequencer

2013 02-14 - ngs webinar - sellappanElsa von Licy

This slidedeck will highlight QIAGEN’s service capabilities in sample isolation, microarray and NGS-sequencing, qPCR panel and custom assay development and bioinformatics as we look at the identification of potential biomarkers and gene signatures. The applications of QIAGEN Service Core in microRNA discovery for toxicology markers in serum and plasma and in identification of RNA signatures for tumor stratification are featured. Learn how you can accelerate your research with QIAGEN service solutions.

Viral genome sequencing

Creative Enzymes

Peter Nagy, Columbia Agilent Symposium, Jan, 27 2012sequencing_columbia

Illumina-General-Overview-Q1-17Matthew Holguin

Coding & Best Practice in Programming in the NGS era

Lex Nederbragt

Digital RNAseq for Gene Expression Profiling: Digital RNAseq Webinar Part 2

QIAGEN

Traditional RNA sequencing (RNA-Seq) is a powerful tool for expression profiling, but is hindered by PCR amplification bias and inaccuracy at low expressing genes. QIAseq RNA is a flexible and precise tool developed for mitigating these complications, allowing digital gene expression analysis. In this webinar we will cover, in depth, the sample requirements, experimental design, NGS platform specific challenges, and workflow for gene enrichment, library prep and sequencing. The applications of QIASeq RNA Panels in cancer research, stem cell differentiation and elucidating the effects small molecules on signaling pathways will be highlighted.

2012 10-24 - ngs webinarElsa von Licy

Clc Bio Basic Company Presentationclcbio

Workshop NGS data analysis - 2

Maté Ongenaert

Rna seq pipeline

Karan Veer Singh

RNA Sequence data analysis,Transcriptome sequencing, Sequencing steady state RNA in a sample is known as RNA-Seq. It is free of limitations such as prior knowledge about the organism is not required. RNA-Seq is useful to unravel inaccessible complexities of transcriptomics such as finding novel transcripts and isoforms. Data set produced is large and complex; interpretation is not straight forward.

Rna seqSean Davis

Introduction to Galaxy and RNA-Seq

Enis Afgan

RNA-seq: Mapping and quality control - part 3

BITS

Sequencing 60,000 Samples: An Innovative Large Cohort Study for Breast Cancer...

QIAGEN

This slidedeck focuses on the design of a large cohort study for assessing breast cancer risk and how an innovative digital sequencing approach is able to solve the previously unmet challenges of this type of NGS study design. Our speaker, Dr. Fergus J. Couch of the Mayo Clinic, presents on the design of this NCI-funded project, which comprises the sequencing of 60,000 samples to assess the risk of breast cancer through association with targeted genes. The design and size of the study requires an accurate, robust and high-throughput sequencing method. The investigators are using a digital DNA sequencing approach from QIAGEN that incorporates molecular barcodes to tag and remove PCR duplicates and increase NGS assay sensitivity. The approach also uses proprietary chemistry that enables uniform sequencing to efficiently utilize sequencing power and deliver optimized results.

The Starbucks Experience

Ethos3

Analysis and Interpretation of Cell-free DNA

QIAGEN

RNA-seq quality control and pre-processing

mikaelhuss

An introduction to RNA-seq data analysis

AGRF_Ltd

AGRF in conjunction with EMBL Australia recently organised a workshop at Monash University Clayton. This workshop was targeted at beginners and biologists who are new to analysing Next-Gen Sequencing data. The workshop also aimed to provide users with a snapshot of bioinformatics and data analysis tips on how to begin to analyse project data. An introduction to RNA-seq data analysis was presented by AGRF Senior Bioinformatician Dr. Sonika Tyagi. Presented: 1st August 2012

What's hot

Biosecurity Challenges in the Genome Engineering Space – Beth Vitalis

Catalyst Biosummit

Genome in a bottle for amp GeT-RM 181030

GenomeInABottle

DNA_ServicesJackie Wright

Customer Case Study: How Novel Compute Technology Transforms Medical and Life...

Amazon Web Services

Accelerate Your Discovery with QIAGEN Service Solutions for Biomarker Researc...

QIAGEN

Viral genome sequencing

Creative Enzymes

Peter Nagy, Columbia Agilent Symposium, Jan, 27 2012sequencing_columbia

Illumina-General-Overview-Q1-17Matthew Holguin

Coding & Best Practice in Programming in the NGS era

Lex Nederbragt

Digital RNAseq for Gene Expression Profiling: Digital RNAseq Webinar Part 2

QIAGEN

2012 10-24 - ngs webinarElsa von Licy

What's hot (11)

Biosecurity Challenges in the Genome Engineering Space – Beth Vitalis

Genome in a bottle for amp GeT-RM 181030

DNA_Services

Customer Case Study: How Novel Compute Technology Transforms Medical and Life...

Accelerate Your Discovery with QIAGEN Service Solutions for Biomarker Researc...

Viral genome sequencing

Peter Nagy, Columbia Agilent Symposium, Jan, 27 2012

Illumina-General-Overview-Q1-17

Coding & Best Practice in Programming in the NGS era

Digital RNAseq for Gene Expression Profiling: Digital RNAseq Webinar Part 2

2012 10-24 - ngs webinar

Viewers also liked

Clc Bio Basic Company Presentationclcbio

Workshop NGS data analysis - 2

Maté Ongenaert

Rna seq pipeline

Karan Veer Singh

Rna seqSean Davis

Introduction to Galaxy and RNA-Seq

Enis Afgan

RNA-seq: Mapping and quality control - part 3

BITS

Sequencing 60,000 Samples: An Innovative Large Cohort Study for Breast Cancer...

QIAGEN

The Starbucks Experience

Ethos3

Analysis and Interpretation of Cell-free DNA

QIAGEN

RNA-seq quality control and pre-processing

mikaelhuss

An introduction to RNA-seq data analysis

AGRF_Ltd

Introduction to RNA-seq and RNA-seq Data Analysis (UEB-UAT Bioinformatics Cou...

VHIR Vall d’Hebron Institut de Recerca

Workshop NGS data analysis - 1

Maté Ongenaert

Microbial Pathogenesis and Host Immune Response

QIAGEN

The research community has begun correlating the makeup of individual microbiomes with disorders and diseases such as obesity, atherosclerosis and cancer. To accomplish this, researchers must first identify and characterize these microbial communities and understand the complex immune interactions between host and pathogen. This webinar provides you with a complete overview of the microbiome, metagenomics and host-pathogen interactions. Experimental strategies, from sample to insight, which can facilitate your microbiology and immunology research, are highlighted.

Next-Generation Sequencing Commercial Milestones Infographic

QIAGEN

Next-generation sequencing (NGS) has revolutionized the way we analyze diseases and commercial outfits such as Illumina, Helicos, QIAGEN and Pacific Biosciences have made significant contributions. In addition, the launch of direct-to-consumer genetic testing solutions has dramatically changed the way consumers access genomics data. Until a few years ago, the cost of sequencing was a major bottleneck. Recent developments have reduced the cost from thousands of dollars to a couple of cents per megabase. When did these changes start? What were the changes in the commercial sector in the last 15 years? This infographic is a timeline of the NGS commercial marketplace.

Introduction to Single-cell RNA-seq

Timothy Tickle

Viewers also liked (16)

Clc Bio Basic Company Presentation

Workshop NGS data analysis - 2

Rna seq pipeline

Rna seq

Introduction to Galaxy and RNA-Seq

RNA-seq: Mapping and quality control - part 3

Sequencing 60,000 Samples: An Innovative Large Cohort Study for Breast Cancer...

The Starbucks Experience

Analysis and Interpretation of Cell-free DNA

RNA-seq quality control and pre-processing

An introduction to RNA-seq data analysis

Introduction to RNA-seq and RNA-seq Data Analysis (UEB-UAT Bioinformatics Cou...

Workshop NGS data analysis - 1

Microbial Pathogenesis and Host Immune Response

Next-Generation Sequencing Commercial Milestones Infographic

Introduction to Single-cell RNA-seq

Elizabeth Buie - Older adults: Are we really designing for our future selves?

Nexer Digital

Enhancing Performance with Globus and the Science DMZ

Globus

Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...

SOFTTECHHUB

The choice of an operating system plays a pivotal role in shaping our computing experience. For decades, Microsoft's Windows has dominated the market, offering a familiar and widely adopted platform for personal and professional use. However, as technological advancements continue to push the boundaries of innovation, alternative operating systems have emerged, challenging the status quo and offering users a fresh perspective on computing. One such alternative that has garnered significant attention and acclaim is Nitrux Linux 3.5.0, a sleek, powerful, and user-friendly Linux distribution that promises to redefine the way we interact with our devices. With its focus on performance, security, and customization, Nitrux Linux presents a compelling case for those seeking to break free from the constraints of proprietary software and embrace the freedom and flexibility of open-source computing.

Generative AI Deep Dive: Advancing from Proof of Concept to Production

Aggregage

GenAISummit 2024 May 28 Sri Ambati Keynote: AGI Belongs to The Community in O...

Sri Ambati

Removing Uninteresting Bytes in Software Fuzzing

Aftab Hussain

Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process. In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds. - These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.

GraphRAG is All You need? LLM & Knowledge Graph

Guy Korland

Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs. 1. Unifying Large Language Models and Knowledge Graphs: A Roadmap. https://arxiv.org/abs/2306.08302 2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs: https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/

Recently uploaded (20)

State of ICS and IoT Cyber Threat Landscape Report 2024 preview

Introduction to CHERI technology - Cybersecurity

Monitoring Java Application Security with JDK Tools and JFR Events

The Art of the Pitch: WordPress Relationships and Sales

By Design, not by Accident - Agile Venture Bolzano 2024

Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdf

FIDO Alliance Osaka Seminar: Passkeys and the Road Ahead.pdf

Epistemic Interaction - tuning interfaces to provide information for AI support

UiPath Test Automation using UiPath Test Suite series, part 4

Encryption in Microsoft 365 - ExpertsLive Netherlands 2024

Essentials of Automations: The Art of Triggers and Actions in FME

Elevating Tactical DDD Patterns Through Object Calisthenics

FIDO Alliance Osaka Seminar: The WebAuthn API and Discoverable Credentials.pdf

Elizabeth Buie - Older adults: Are we really designing for our future selves?

Enhancing Performance with Globus and the Science DMZ

Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...

Generative AI Deep Dive: Advancing from Proof of Concept to Production

GenAISummit 2024 May 28 Sri Ambati Keynote: AGI Belongs to The Community in O...

Removing Uninteresting Bytes in Software Fuzzing

GraphRAG is All You need? LLM & Knowledge Graph

CLC bio presentation at 5th SFAF 6/3/2010

1. CLC bio A Comprehensive Platform for NGS Data Analysis Saul A. Kravitz, PhD Director of Consulting Services

2. Before the Flood 2005: $5M Human genome – 19 sequencer years Sample Prep Analysis Sequencing Science

3. Nextgen Sequencing Revolution 2010: $6k Human genome ~1 sequencer day Help!! Sample Prep Analysis Sequencing Science

5. GUI-driven

6. HPC integration

7. Unprecedented data volumes

8. Rapid technology change, applications growth

9. Multi-platform data integration

10. No one-size-fits-all solutions

11.

12. Swiss Army Knife of NGS Analysis SDK Intuitive GUI Traditional Bioinformatics Visualization Desktop Solutions EnterpriseSolutions High Performance File Format Conversion Tools Integration Epigenomics Transcriptomics Genomics RNA-Seq miRNA Read Mapping De Novo Assembly SNP/DIP Detection CHIP-Seq

13. Why not use free tools? Are tools free or “free”? Tools vs solutions True cost of ownership Ease of Use Tools integration Support

14. Small RNA Analysis(in Beta soon) Identify and filter/trim adapters annotate using mirBASE and other resources - target species of interest Merge/group by mature, precursor/reference Fully integrated with expression analysis

15. De Novo Assembler Human assembly of 38x Illumina paired-end CLC Quality equivalent to Abyss CLC: 7 hrs, 1 node, 42 Gbof RAM Abyss: 80 hrs, 21 nodes, 336 Gbof RAM Metagenomics Assembly METAHIT Dataset MH0041 40M 75bp paired end 3 hrs on desktop, 6 Gb RAM Higher N50 and Total Contig Size than Reported

16. Viral Sequencing at JCVI(See Nadia Fedorova’s Poster!) Amplify and Barcode using SISPA, 454 + Illumina Sequencing Depth of coverage sometimes >1000x De novo Assembly of Consensus for all Segments For each segment: Map reads from each technology independently using best full length reference from NCBI, call variations Update reference with variations confirmed by multiple technologies Map reads using updated reference and all reads Convert to consed, analyze, order Sanger closure reactions Source: Jessica Hostetler, Nadia Federova, Tim Stockwell, Danny Katzel

17. Why CLC bioTools? CLC handled hybrid sequencing technologies directly Very biased coverage confounded other assemblers that expect random arrival stats. CLC didn’t seem to suffer from biased coverage. Very accurate SNP calls in areas of deep coverage. Tim Stockwell Director of Viral Informatics J. Craig Venter Institute

18. Targeted Resequencing QC Assessment of targeted sequencing technology Coverage Statistics for Targeted Regions Very short schedule, limited bioinformatics staff Plug-in development leveraging CLC tools to automate the process and meet short deadline QC Report now available as plug-in

19. Professional Services Developing customized solutions Integration with LIMS, workflows, DB Bioinformatics Algorithm Development Cloud and Grid Integration Data Analysis

20. Questions? Saul A. Kravitz, PhD skravitz@clcbio.com (301)355-0813 Thank you for listening

21. Questions Saul A. Kravitz, PhD skravitz @ clcbio.com 301)355-0813 Thank you for listening

Editor's Notes

GUI-driven tools and workflows
- miRNA workflow leveraging mirBASE and other resources
Very fast, small memory footprint
SISPA = Sequence Independent Single Primer Amplification (if that needs spelling out) – amplifies and barcodes DNA moleculesAlso, if people are interested, can also mention availability of Danny Katzel’s cas2consed software.
CustomizationJava plug-in architecture for Server and WorkbenchOptimized “Cell” command line tools for efficient HPCWizard-based integration of customer toolsServer integration via SOAP and Command Line*

CLC bio presentation at 5th SFAF 6/3/2010

Recommended

Recommended

More Related Content

What's hot

What's hot (11)

Viewers also liked

Viewers also liked (16)

Similar to CLC bio presentation at 5th SFAF 6/3/2010

Similar to CLC bio presentation at 5th SFAF 6/3/2010 (20)

Recently uploaded

Recently uploaded (20)

CLC bio presentation at 5th SFAF 6/3/2010

Editor's Notes