INTRODUCTION TO NGS VARIANT CALLING ANALYSIS
|
|
- Verity Atkins
- 7 years ago
- Views:
Transcription
1 Hospital Universitari Vall d Hebron Institut de Recerca - VHIR Institut d Investigació Sanitària de l Instituto de Salud Carlos III (ISCIII) INTRODUCTION TO NGS VARIANT CALLING ANALYSIS Bioinformàtica per la Recerca Biomèdica Ferran Briansó ferran.brianso@vhir.org 15/05/201
2 PRESENTATION OUTLINE 1 1. NGS WORKFLOW OVERVIEW 2 2. WET LAB STEPS 3 3. IMPORTANT SEQUENCING CONCEPTS. NGS ANALYSIS WORKFLOW 5 1. Primary analysis: de-multiplexing, QC 2. Secondary analysis: read mapping and variant calling 3. Tertiary analysis: annotation, filtering VISUALIZATION 6 6. COMMON PIPELINES AND FORMATS 7 7. CONCLUSIONS
3 1 NGS WORKFLOW OVERVIEW Extracted from Dr Kassahn's publicly shared slides (2013) 3
4 2 LIBRARY PREPARATION Select target Hybridization-based cature or PCR Add adapters Contain binding sequences Barcodes Primer sequences Amplify material
5 2 LIBRARY PREPARATION Select target Hybridization-based cature or PCR Add adapters Contain binding sequences Barcodes Primer sequences Amplify material A) Fragment DNA B) End-repair C) A-tailing, adapter ligation and PCR D) Final library contains sample insert indices (barcodes) flowcell binding sequences primer binding sequences 5
6 2 LIBRARY PREPARATION Select target Hybridization-based cature or PCR Add adapters Contain binding sequences Barcodes Primer sequences Amplify material 6
7 2 TEMPLATE PREPARATION Attachment of library e.g. To Illumina Flowcell Amplification of library molecules e.g. Brigde amplification 7
8 2 BRIDGE AMPLIFICATION 8
9 2 SEQUENCING Sequencing-by-Synthesis Detection by: Illumina fluorescence Ion Torrent ph ROCHE 5 PO and light 9
10 2 SEQUENCING-BY-SYNTHESIS (ILLUMINA) 10
11 1 3 IMPORTANT SEQUENCING CONCEPTS Barcoding/Indexing: allows multiplexing of different samples Single-end vs paired-end sequencing Coverage: avg. number reads per target Quality scores (Qscore): log-scales! 11
12 NGS DATA ANALYSIS WORKFLOW 12
13 DE-MULTIPLEXING (BARCODE SPLITTING) 13
14 FASTQ FORMAT see en.wikipedia.org/wiki/fastq_format 1
15 SEQUENCE QUALITY: fastqc Details of the output 15
16 NGS DATA ANALYSIS WORKFLOW 16
17 READ MAPPING (BASIC ALIGNMENT) Comparison against reference genome (! not assembly!) Many aligners (short reads, longer reads, RNAseq...) Examples: BWA, Bowtie SAM/BAM files 17
18 BURROWS-WHEELER ALIGNMENT TOOL (BWA) Popular tool for genomic sequence data (not RNASeq!) Li and Durbin 2009 Bioinformatics Challenge: compare billion of short sequence reads (.fastq file) against human genome (3Gb) Burrows-Wheeler Transform to index the human genome and allow memory-efficient and fast string matching between sequence read and reference genome Li & Durbin 2009 Bionformatics 18
19 SAM/BAM FILES see 19
20 SAM/BAM Header (information regarding reference genome, alignment method...) 1) Read ID (QNAME) 2) Bitwise FLAG (first/second read in pair, both reads mapped...) 3) ReferenceSequence Name (RNAME) ) Position (POS, coordinate) 5) MapQuality (MAPQ = -10log10P[wrong mapping position]) 6) CIGAR (describes alignment matches, skipped regions, insertions..) 7) ReferenceSequence (RNEXT, Ref seq of the pair) 8) Position of the pair (PNEXT) 9) TemplateLength (TLEN) 10) ReadSequence 11) QUAL (in Fastq format, '*' if NA)... 20
21 VARIANT CALLING Identify sequence variants Distinguish signal vs noise VCF files Examples: SAMtools, SNVmix 21
22 SEQUENCE VARIANTS Differences to the reference 22
23 SEQUENCE VARIANTS Sanger: is it real?? NGS: read count Provides confidence (statistics!) Sensitivity tune-able parameter (dependent on coverage) 23
24 VARIANT CALLING: GATK Genome Analysis Toolkit (BROAD Institute) Initially developed for 1000 Genomes Project Single or multiple sample analysis (cohort) Popular tool for germline variant calling Evaluates probability of genotype given read data see and McKenna et al. Genome Research
25 SOMATIC VARIANT CALLING Somatic mutations can occur at low freq. (<10%) due to: Tumor heterogeneity (multiple clones) Low tumor purity (% normal cells in tumor sample) Requires different thresholds than germline variant calling when evaluating signal vs noise Trade-off between sensitivity (ability to detect mutation) and specificity (rate of false positives) Nature Reviews Cancer 12, (May 2012) 25
26 1 INDELS DETECTION Small insertions/ deletions The trouble with mapping approaches modified from Heng Li (Broad Institute) 26
27 INDELS DETECTION Small insertions/ deletions The trouble with mapping approaches 27
28 INDELS DETECTION Small insertions/ deletions The trouble with mapping approaches 28
29 RE-ALIGNMENT Re-align considering multi-read context, SNPs & INDELS previous info... adapted from Andreas Schreiber 29
30 EVALUATING VARIANT QUALITY TAKING INTO ACCOUNT: Coverage at position Number independent reads supporting variant Observed allele fraction vs expected (somatic / germline) Strand bias Base qualities at variant position Mapping qualities of reads supporting variant Variant position within reads (near ends or at centre) 30
31 VCF FILES Variant Call Format Standard for reporting variants from NGS Describes metadata of analysis and variant calls Text file format (open in Text Editor or Excel)!!! Not a MS Office vcard!!! see -version-1 31
32 VCF FILES 32
33 NGS DATA ANALYSIS WORKFLOW 33
34 VARIANT ANNOTATION Provide biological & clinical context Identify disease-causing mutations (among 1000s of variants) 3
35 ANNOTATION OVERVIEW 35
36 VARIANT FILTERING AND PRIORIZATION COMMON STEPS: PURPOSE: Identify pathogenic or disease-associated mutation(s) Reduce candidate variants to reportable set Remove poor quality variant calls Remove common polymorphisms Prioritize variants with high functional impact Compare against known disease genes Consider mode of inheritance (autosomal recessive, X-linked...) Consider segregation in family (where multiple samples available) 36
37 5 NGS DATA ANALYSIS WORKFLOW 37
38 5 VISUALIZATION IGV (or Genome Browser, Circos...) provided by Katherine Pillman 38
39 6 COMMON PIPELINE bcl2fastq (Illumina) FastQC (open-source) Exomes (HiSeq): BWA(open-source), GATK (Broad) Gene panels (MiSeq, PGM): MiSeq Reporter (Illumina) Torrent Suite (Ion Torrent) Custom scripts and third party tools (Annovar, snpeff, PolyPhen, SIFT...) Commercial annotation software (GeneticistAssistant, VariantStudio...) 39
40 6 COMMON DATA FORMATS.bcl.fastq.BAM.VCF.csv.txt.xls.html... 0
41 7 CONCLUSIONS NGS data - the new currency of (molecular) biology Broad applications (ecology, evolution, ag sciences, medical research and clinical diagnostics...). Rapidly evolving (sequencing technologies, library preparation methods, analysis approaches, software). Different tools/pipelines/parametrization gives different results, (more standards needed). Bioinformatics pipelines typically combine vendor software, third-party tools and custom scripts. Requires skills in scripting, Linux/Unix, HPC. Requires advanced hardware (not always available). Understanding of data (SE, PE, RNA-Seq) important for successful analysis. 1
Introduction to NGS data analysis
Introduction to NGS data analysis Jeroen F. J. Laros Leiden Genome Technology Center Department of Human Genetics Center for Human and Clinical Genetics Sequencing Illumina platforms Characteristics: High
More informationData Analysis for Ion Torrent Sequencing
IFU022 v140202 Research Use Only Instructions For Use Part III Data Analysis for Ion Torrent Sequencing MANUFACTURER: Multiplicom N.V. Galileilaan 18 2845 Niel Belgium Revision date: August 21, 2014 Page
More informationNazneen Aziz, PhD. Director, Molecular Medicine Transformation Program Office
2013 Laboratory Accreditation Program Audioconferences and Webinars Implementing Next Generation Sequencing (NGS) as a Clinical Tool in the Laboratory Nazneen Aziz, PhD Director, Molecular Medicine Transformation
More informationIntroduction to next-generation sequencing data
Introduction to next-generation sequencing data David Simpson Centre for Experimental Medicine Queens University Belfast http://www.qub.ac.uk/research-centres/cem/ Outline History of DNA sequencing NGS
More informationNext Generation Sequencing: Technology, Mapping, and Analysis
Next Generation Sequencing: Technology, Mapping, and Analysis Gary Benson Computer Science, Biology, Bioinformatics Boston University gbenson@bu.edu http://tandem.bu.edu/ The Human Genome Project took
More informationDelivering the power of the world s most successful genomics platform
Delivering the power of the world s most successful genomics platform NextCODE Health is bringing the full power of the world s largest and most successful genomics platform to everyday clinical care NextCODE
More informationTargeted. sequencing solutions. Accurate, scalable, fast TARGETED
Targeted TARGETED Sequencing sequencing solutions Accurate, scalable, fast Sequencing for every lab, every budget, every application Ion Torrent semiconductor sequencing Ion Torrent technology has pioneered
More informationFocusing on results not data comprehensive data analysis for targeted next generation sequencing
Focusing on results not data comprehensive data analysis for targeted next generation sequencing Daniel Swan, Jolyon Holdstock, Angela Matchan, Richard Stark, John Shovelton, Duarte Mohla and Simon Hughes
More informationTutorial for Windows and Macintosh. Preparing Your Data for NGS Alignment
Tutorial for Windows and Macintosh Preparing Your Data for NGS Alignment 2015 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Ann Arbor, MI 48108 USA 1.800.497.4939 (USA) 1.734.769.7249
More informationAnalysis of NGS Data
Analysis of NGS Data Introduction and Basics Folie: 1 Overview of Analysis Workflow Images Basecalling Sequences denovo - Sequencing Assembly Annotation Resequencing Alignments Comparison to reference
More informationAn example of bioinformatics application on plant breeding projects in Rijk Zwaan
An example of bioinformatics application on plant breeding projects in Rijk Zwaan Xiangyu Rao 17-08-2012 Introduction of RZ Rijk Zwaan is active worldwide as a vegetable breeding company that focuses on
More informationNext generation DNA sequencing technologies. theory & prac-ce
Next generation DNA sequencing technologies theory & prac-ce Outline Next- Genera-on sequencing (NGS) technologies overview NGS applica-ons NGS workflow: data collec-on and processing the exome sequencing
More informationHow-To: SNP and INDEL detection
How-To: SNP and INDEL detection April 23, 2014 Lumenogix NGS SNP and INDEL detection Mutation Analysis Identifying known, and discovering novel genomic mutations, has been one of the most popular applications
More informationText file One header line meta information lines One line : variant/position
Software Calling: GATK SAMTOOLS mpileup Varscan SOAP VCF format Text file One header line meta information lines One line : variant/position ##fileformat=vcfv4.1! ##filedate=20090805! ##source=myimputationprogramv3.1!
More informationThe Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics
The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics The GS Junior System The Power of Next-Generation Sequencing on Your Benchtop Proven technology: Uses the same long
More informationSingle-Cell Whole Genome Sequencing on the C1 System: a Performance Evaluation
PN 100-9879 A1 TECHNICAL NOTE Single-Cell Whole Genome Sequencing on the C1 System: a Performance Evaluation Introduction Cancer is a dynamic evolutionary process of which intratumor genetic and phenotypic
More informationG E N OM I C S S E RV I C ES
GENOMICS SERVICES THE NEW YORK GENOME CENTER NYGC is an independent non-profit implementing advanced genomic research to improve diagnosis and treatment of serious diseases. capabilities. N E X T- G E
More informationNew generation sequencing: current limits and future perspectives. Giorgio Valle CRIBI - Università di Padova
New generation sequencing: current limits and future perspectives Giorgio Valle CRIBI Università di Padova Around 2004 the Race for the 1000$ Genome started A few questions... When? How? Why? Standard
More informationSEQUENCING. From Sample to Sequence-Ready
SEQUENCING From Sample to Sequence-Ready ACCESS ARRAY SYSTEM HIGH-QUALITY LIBRARIES, NOT ONCE, BUT EVERY TIME The highest-quality amplicons more sensitive, accurate, and specific Full support for all major
More informationNext Generation Sequencing
Next Generation Sequencing Technology and applications 10/1/2015 Jeroen Van Houdt - Genomics Core - KU Leuven - UZ Leuven 1 Landmarks in DNA sequencing 1953 Discovery of DNA double helix structure 1977
More informationComparing Methods for Identifying Transcription Factor Target Genes
Comparing Methods for Identifying Transcription Factor Target Genes Alena van Bömmel (R 3.3.73) Matthew Huska (R 3.3.18) Max Planck Institute for Molecular Genetics Folie 1 Transcriptional Regulation TF
More informationSingle-Cell DNA Sequencing with the C 1. Single-Cell Auto Prep System. Reveal hidden populations and genetic diversity within complex samples
DATA Sheet Single-Cell DNA Sequencing with the C 1 Single-Cell Auto Prep System Reveal hidden populations and genetic diversity within complex samples Single-cell sensitivity Discover and detect SNPs,
More informationGenotyping by sequencing and data analysis. Ross Whetten North Carolina State University
Genotyping by sequencing and data analysis Ross Whetten North Carolina State University Stein (2010) Genome Biology 11:207 More New Technology on the Horizon Genotyping By Sequencing Timeline 2007 Complexity
More informationPreciseTM Whitepaper
Precise TM Whitepaper Introduction LIMITATIONS OF EXISTING RNA-SEQ METHODS Correctly designed gene expression studies require large numbers of samples, accurate results and low analysis costs. Analysis
More informationCore Facility Genomics
Core Facility Genomics versatile genome or transcriptome analyses based on quantifiable highthroughput data ascertainment 1 Topics Collaboration with Harald Binder and Clemens Kreutz Project: Microarray
More informationShouguo Gao Ph. D Department of Physics and Comprehensive Diabetes Center
Computational Challenges in Storage, Analysis and Interpretation of Next-Generation Sequencing Data Shouguo Gao Ph. D Department of Physics and Comprehensive Diabetes Center Next Generation Sequencing
More informationNGS data analysis. Bernardo J. Clavijo
NGS data analysis Bernardo J. Clavijo 1 A brief history of DNA sequencing 1953 double helix structure, Watson & Crick! 1977 rapid DNA sequencing, Sanger! 1977 first full (5k) genome bacteriophage Phi X!
More informationAbout the Princess Margaret Computational Biology Resource Centre (PMCBRC) cluster
Cluster Info Sheet About the Princess Margaret Computational Biology Resource Centre (PMCBRC) cluster Welcome to the PMCBRC cluster! We are happy to provide and manage this compute cluster as a resource
More informationSeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications
Product Bulletin Sequencing Software SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications Comprehensive reference sequence handling Helps interpret the role of each
More informationAssuring the Quality of Next-Generation Sequencing in Clinical Laboratory Practice. Supplementary Guidelines
Assuring the Quality of Next-Generation Sequencing in Clinical Laboratory Practice Next-generation Sequencing: Standardization of Clinical Testing (Nex-StoCT) Workgroup Principles and Guidelines Supplementary
More informationUsing Illumina BaseSpace Apps to Analyze RNA Sequencing Data
Using Illumina BaseSpace Apps to Analyze RNA Sequencing Data The Illumina TopHat Alignment and Cufflinks Assembly and Differential Expression apps make RNA data analysis accessible to any user, regardless
More informationMiSeq: Imaging and Base Calling
MiSeq: Imaging and Page Welcome Navigation Presenter Introduction MiSeq Sequencing Workflow Narration Welcome to MiSeq: Imaging and. This course takes 35 minutes to complete. Click Next to continue. Please
More informationLifeScope Genomic Analysis Software 2.5
USER GUIDE LifeScope Genomic Analysis Software 2.5 Graphical User Interface DATA ANALYSIS METHODS AND INTERPRETATION Publication Part Number 4471877 Rev. A Revision Date November 2011 For Research Use
More informationPractical Guideline for Whole Genome Sequencing
Practical Guideline for Whole Genome Sequencing Disclosure Kwangsik Nho Assistant Professor Center for Neuroimaging Department of Radiology and Imaging Sciences Center for Computational Biology and Bioinformatics
More information8/7/2012. Experimental Design & Intro to NGS Data Analysis. Examples. Agenda. Shoe Example. Breast Cancer Example. Rat Example (Experimental Design)
Experimental Design & Intro to NGS Data Analysis Ryan Peters Field Application Specialist Partek, Incorporated Agenda Experimental Design Examples ANOVA What assays are possible? NGS Analytical Process
More informationGenetic Analysis. Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis
Genetic Analysis Phenotype analysis: biological-biochemical analysis Behaviour under specific environmental conditions Behaviour of specific genetic configurations Behaviour of progeny in crosses - Genotype
More informationBRCA1 / 2 testing by massive sequencing highlights, shadows or pitfalls?
BRCA1 / 2 testing by massive sequencing highlights, shadows or pitfalls? Giovanni Luca Scaglione, PhD ------------------------ Laboratory of Clinical Molecular Diagnostics and Personalized Medicine, Institute
More informationTGC AT YOUR SERVICE. Taking your research to the next generation
TGC AT YOUR SERVICE Taking your research to the next generation 1. TGC At your service 2. Applications of Next Generation Sequencing 3. Experimental design 4. TGC workflow 5. Sample preparation 6. Illumina
More informationData Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms
Data Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms Introduction Mate pair sequencing enables the generation of libraries with insert sizes in the range of several kilobases (Kb).
More informationDisease gene identification with exome sequencing
Disease gene identification with exome sequencing Christian Gilissen Dept. of Human Genetics Radboud University Nijmegen Medical Centre c.gilissen@antrg.umcn.nl Contents Infrastructure Exome sequencing
More informationLeading Genomics. Diagnostic. Discove. Collab. harma. Shanghai Cambridge, MA Reykjavik
Leading Genomics Diagnostic harma Discove Collab Shanghai Cambridge, MA Reykjavik Global leadership for using the genome to create better medicine WuXi NextCODE provides a uniquely proven and integrated
More informationAdvances in RainDance Sequence Enrichment Technology and Applications in Cancer Research. March 17, 2011 Rendez-Vous Séquençage
Advances in RainDance Sequence Enrichment Technology and Applications in Cancer Research March 17, 2011 Rendez-Vous Séquençage Presentation Overview Core Technology Review Sequence Enrichment Application
More informationData Analysis & Management of High-throughput Sequencing Data. Quoclinh Nguyen Research Informatics Genomics Core / Medical Research Institute
Data Analysis & Management of High-throughput Sequencing Data Quoclinh Nguyen Research Informatics Genomics Core / Medical Research Institute Current Issues Current Issues The QSEQ file Number files per
More informationHow Sequencing Experiments Fail
How Sequencing Experiments Fail v1.0 Simon Andrews simon.andrews@babraham.ac.uk Classes of Failure Technical Tracking Library Contamination Biological Interpretation Something went wrong with a machine
More informationNext generation sequencing (NGS)
Next generation sequencing (NGS) Vijayachitra Modhukur BIIT modhukur@ut.ee 1 Bioinformatics course 11/13/12 Sequencing 2 Bioinformatics course 11/13/12 Microarrays vs NGS Sequences do not need to be known
More informationACMG clinical laboratory standards for next-generation sequencing
American College of Medical Genetics and Genomics ACMG Practice Guidelines ACMG clinical laboratory standards for next-generation sequencing Heidi L. Rehm, PhD 1,2, Sherri J. Bale, PhD 3, Pinar Bayrak-Toydemir,
More informationHistory of DNA Sequencing & Current Applications
History of DNA Sequencing & Current Applications Christopher McLeod President & CEO, 454 Life Sciences, A Roche Company IMPORTANT NOTICE Intended Use Unless explicitly stated otherwise, all Roche Applied
More informationTruSeq Custom Amplicon v1.5
Data Sheet: Targeted Resequencing TruSeq Custom Amplicon v1.5 A new and improved amplicon sequencing solution for interrogating custom regions of interest. Highlights Figure 1: TruSeq Custom Amplicon Workflow
More informationNew solutions for Big Data Analysis and Visualization
New solutions for Big Data Analysis and Visualization From HPC to cloud-based solutions Barcelona, February 2013 Nacho Medina imedina@cipf.es http://bioinfo.cipf.es/imedina Head of the Computational Biology
More informationGenetic diagnostics the gateway to personalized medicine
Micronova 20.11.2012 Genetic diagnostics the gateway to personalized medicine Kristiina Assoc. professor, Director of Genetic Department HUSLAB, Helsinki University Central Hospital The Human Genome Packed
More informationRNA-Seq Tutorial 1. John Garbe Research Informatics Support Systems, MSI March 19, 2012
RNA-Seq Tutorial 1 John Garbe Research Informatics Support Systems, MSI March 19, 2012 Tutorial 1 RNA-Seq Tutorials RNA-Seq experiment design and analysis Instruction on individual software will be provided
More informationAnalysis of ChIP-seq data in Galaxy
Analysis of ChIP-seq data in Galaxy November, 2012 Local copy: https://galaxy.wi.mit.edu/ Joint project between BaRC and IT Main site: http://main.g2.bx.psu.edu/ 1 Font Conventions Bold and blue refers
More informationHENIPAVIRUS ANTIBODY ESCAPE SEQUENCING REPORT
HENIPAVIRUS ANTIBODY ESCAPE SEQUENCING REPORT Kimberly Bishop Lilly 1,2, Truong Luu 1,2, Regina Cer 1,2, and LT Vishwesh Mokashi 1 1 Naval Medical Research Center, NMRC Frederick, 8400 Research Plaza,
More informationGenomic Testing: Actionability, Validation, and Standard of Lab Reports
Genomic Testing: Actionability, Validation, and Standard of Lab Reports emerge: Laura Rasmussen-Torvik Reaction: Heidi Rehm Summary: Dick Weinshilboum Panel: Murray Brilliant, David Carey, John Carpten,
More informationHiSeq Analysis Software v0.9 User Guide
HiSeq Analysis Software v0.9 User Guide FOR RESEARCH USE ONLY Quick Start 4 Introduction 5 Enrichment Analysis Workflow 6 Whole Genome Sequencing Analysis Workflow 8 Additional Software 12 Installing HiSeq
More informationOverview of Next Generation Sequencing platform technologies
Overview of Next Generation Sequencing platform technologies Dr. Bernd Timmermann Next Generation Sequencing Core Facility Max Planck Institute for Molecular Genetics Berlin, Germany Outline 1. Technologies
More informationIntroduction to transcriptome analysis using High Throughput Sequencing technologies (HTS)
Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS) A typical RNA Seq experiment Library construction Protocol variations Fragmentation methods RNA: nebulization,
More informationGo where the biology takes you. Genome Analyzer IIx Genome Analyzer IIe
Go where the biology takes you. Genome Analyzer IIx Genome Analyzer IIe Go where the biology takes you. To published results faster With proven scalability To the forefront of discovery To limitless applications
More informationBioinformatics Unit Department of Biological Services. Get to know us
Bioinformatics Unit Department of Biological Services Get to know us Domains of Activity IT & programming Microarray analysis Sequence analysis Bioinformatics Team Biostatistical support NGS data analysis
More informationLectures 1 and 8 15. February 7, 2013. Genomics 2012: Repetitorium. Peter N Robinson. VL1: Next- Generation Sequencing. VL8 9: Variant Calling
Lectures 1 and 8 15 February 7, 2013 This is a review of the material from lectures 1 and 8 14. Note that the material from lecture 15 is not relevant for the final exam. Today we will go over the material
More informationBioHPC Web Computing Resources at CBSU
BioHPC Web Computing Resources at CBSU 3CPG workshop Robert Bukowski Computational Biology Service Unit http://cbsu.tc.cornell.edu/lab/doc/biohpc_web_tutorial.pdf BioHPC infrastructure at CBSU BioHPC Web
More informationCRAC: An integrated approach to analyse RNA-seq reads Additional File 3 Results on simulated RNA-seq data.
: An integrated approach to analyse RNA-seq reads Additional File 3 Results on simulated RNA-seq data. Nicolas Philippe and Mikael Salson and Thérèse Commes and Eric Rivals February 13, 2013 1 Results
More informationBuilding Highly-Optimized, Low-Latency Pipelines for Genomic Data Analysis
Building Highly-Optimized, Low-Latency Pipelines for Genomic Data Analysis Yanlei Diao, Abhishek Roy University of Massachusetts Amherst {yanlei,aroy}@cs.umass.edu Toby Bloom New York Genome Center tbloom@nygenome.org
More informationDeep Sequencing Data Analysis
Deep Sequencing Data Analysis Ross Whetten Professor Forestry & Environmental Resources Background Who am I, and why am I teaching this topic? I am not an expert in bioinformatics I started as a biologist
More informationAutomated DNA sequencing 20/12/2009. Next Generation Sequencing
DNA sequencing the beginnings Ghent University (Fiers et al) pioneers sequencing first complete gene (1972) first complete genome (1976) Next Generation Sequencing Fred Sanger develops dideoxy sequencing
More informationServices. Updated 05/31/2016
Updated 05/31/2016 Services 1. Whole exome sequencing... 2 2. Whole Genome Sequencing (WGS)... 3 3. 16S rrna sequencing... 4 4. Customized gene panels... 5 5. RNA-Seq... 6 6. qpcr... 7 7. HLA typing...
More informationIntroduction To Epigenetic Regulation: How Can The Epigenomics Core Services Help Your Research? Maria (Ken) Figueroa, M.D. Core Scientific Director
Introduction To Epigenetic Regulation: How Can The Epigenomics Core Services Help Your Research? Maria (Ken) Figueroa, M.D. Core Scientific Director Gene expression depends upon multiple factors Gene Transcription
More informationSMRT Analysis v2.2.0 Overview. 1. SMRT Analysis v2.2.0. 1.1 SMRT Analysis v2.2.0 Overview. Notes:
SMRT Analysis v2.2.0 Overview 100 338 400 01 1. SMRT Analysis v2.2.0 1.1 SMRT Analysis v2.2.0 Overview Welcome to Pacific Biosciences' SMRT Analysis v2.2.0 Overview 1.2 Contents This module will introduce
More informationSAP HANA Enabling Genome Analysis
SAP HANA Enabling Genome Analysis Joanna L. Kelley, PhD Postdoctoral Scholar, Stanford University Enakshi Singh, MSc HANA Product Management, SAP Labs LLC Outline Use cases Genomics review Challenges in
More informationNext Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Genes 2012, 3, 545-575; doi:10.3390/genes3030545 Article OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline
More informationHow many of you have checked out the web site on protein-dna interactions?
How many of you have checked out the web site on protein-dna interactions? Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. Find and be ready to discuss
More informationPractical Solutions for Big Data Analytics
Practical Solutions for Big Data Analytics Ravi Madduri Computation Institute (madduri@anl.gov) Paul Dave (pdave@uchicago.edu) Dinanath Sulakhe (sulakhe@uchicago.edu) Alex Rodriguez (arodri7@uchicago.edu)
More informationBuilding Bioinformatics Capacity in Africa. Nicky Mulder CBIO Group, UCT
Building Bioinformatics Capacity in Africa Nicky Mulder CBIO Group, UCT Outline What is bioinformatics? Why do we need IT infrastructure? What e-infrastructure does it require? How we are developing this
More informationRETRIEVING SEQUENCE INFORMATION. Nucleotide sequence databases. Database search. Sequence alignment and comparison
RETRIEVING SEQUENCE INFORMATION Nucleotide sequence databases Database search Sequence alignment and comparison Biological sequence databases Originally just a storage place for sequences. Currently the
More informationGlobus Genomics Tutorial GlobusWorld 2014
Globus Genomics Tutorial GlobusWorld 2014 Agenda Overview of Globus Genomics Example Collaborations Demonstration Globus Genomics interface Globus Online integration Scenario 1: Using Globus Genomics for
More informationReduced Representation Bisulfite-Seq A Brief Guide to RRBS
April 17, 2013 Reduced Representation Bisulfite-Seq A Brief Guide to RRBS What is RRBS? Typically, RRBS samples are generated by digesting genomic DNA with the restriction endonuclease MspI. This is followed
More informationVersion 5.0 Release Notes
Version 5.0 Release Notes 2011 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Ann Arbor, MI 48108 USA 1.800.497.4939 (USA) +1.734.769.7249 (elsewhere) +1.734.769.7074 (fax) www.genecodes.com
More informationUGENE Quick Start Guide
Quick Start Guide This document contains a quick introduction to UGENE. For more detailed information, you can find the UGENE User Manual and other special manuals in project website: http://ugene.unipro.ru.
More informationComputational Genomics. Next generation sequencing (NGS)
Computational Genomics Next generation sequencing (NGS) Sequencing technology defies Moore s law Nature Methods 2011 Log 10 (price) Sequencing the Human Genome 2001: Human Genome Project 2.7G$, 11 years
More informationOncology Insights Enabled by Knowledge Base-Guided Panel Design and the Seamless Workflow of the GeneReader NGS System
White Paper Oncology Insights Enabled by Knowledge Base-Guided Panel Design and the Seamless Workflow of the GeneReader NGS System Abstract: This paper describes QIAGEN s philosophy and process for developing
More informationGenome Sequencer System. Amplicon Sequencing. Application Note No. 5 / February 2007. www.roche-applied-science.com
Genome Sequencer System Application Note No. 5 / February 2007 Amplicon Sequencing www.roche-applied-science.com 1 Amplicon Sequencing Corresponding author: Tom Jarvie, 454 Life Sciences Corporation, Branford,
More informationFOR REFERENCE PURPOSES
BIOO LIFE SCIENCE PRODUCTS FOR REFERENCE PURPOSES This manual is for Reference Purposes Only. DO NOT use this protocol to run your assays. Periodically, optimizations and revisions are made to the kit
More informationBIOL 3200 Spring 2015 DNA Subway and RNA-Seq Data Analysis
BIOL 3200 Spring 2015 DNA Subway and RNA-Seq Data Analysis By the end of this lab students should be able to: Describe the uses for each line of the DNA subway program (Red/Yellow/Blue/Green) Describe
More informationNew Technologies for Sensitive, Low-Input RNA-Seq. Clontech Laboratories, Inc.
New Technologies for Sensitive, Low-Input RNA-Seq Clontech Laboratories, Inc. Outline Introduction Single-Cell-Capable mrna-seq Using SMART Technology SMARTer Ultra Low RNA Kit for the Fluidigm C 1 System
More informationNext Generation Sequencing for DUMMIES
Next Generation Sequencing for DUMMIES Looking at a presentation without the explanation from the author is sometimes difficult to understand. This document contains extra information for some slides that
More informationBig data in cancer research : DNA sequencing and personalised medicine
Big in cancer research : DNA sequencing and personalised medicine Philippe Hupé Conférence BIGDATA 04/04/2013 1 - Titre de la présentation - nom du département émetteur et/ ou rédacteur - 00/00/2005 Deciphering
More informationQ&A: Kevin Shianna on Ramping up Sequencing for the New York Genome Center
Q&A: Kevin Shianna on Ramping up Sequencing for the New York Genome Center Name: Kevin Shianna Age: 39 Position: Senior vice president, sequencing operations, New York Genome Center, since July 2012 Experience
More informationAnalysis of DNA methylation: bisulfite libraries and SOLiD sequencing
Analysis of DNA methylation: bisulfite libraries and SOLiD sequencing An easy view of the bisulfite approach CH3 genome TAGTACGTTGAT TAGTACGTTGAT read TAGTACGTTGAT TAGTATGTTGAT Three main problems 1.
More informationSRA File Formats Guide
SRA File Formats Guide Version 1.1 10 Mar 2010 National Center for Biotechnology Information National Library of Medicine EMBL European Bioinformatics Institute DNA Databank of Japan 1 Contents SRA File
More informationTowards Integrating the Detection of Genetic Variants into an In-Memory Database
Towards Integrating the Detection of Genetic Variants into an 2nd International Workshop on Big Data in Bioinformatics and Healthcare Oct 27, 2014 Motivation Genome Data Analysis Process DNA Sample Base
More informationDescription: Molecular Biology Services and DNA Sequencing
Description: Molecular Biology s and DNA Sequencing DNA Sequencing s Single Pass Sequencing Sequence data only, for plasmids or PCR products Plasmid DNA or PCR products Plasmid DNA: 20 100 ng/μl PCR Product:
More informationAll in a highly interactive, easy to use Windows environment.
Database Providing: Accessibility Security Quality Control Review Variant Review Historical Library Variant Pathogenicity Prediction Laboratory Reporting Exportation to LIMS All in a highly interactive,
More informationA Hitchhiker s Guide to Next-Generation Sequencing
A Hitchhiker s Guide to Next-Generation Sequencing by Gabe Rudy, VP of Product Development If you have had any experience with Golden Helix, you know we are not a company to shy away from a challenge.
More informationSingle Nucleotide Polymorphisms (SNPs)
Single Nucleotide Polymorphisms (SNPs) Additional Markers 13 core STR loci Obtain further information from additional markers: Y STRs Separating male samples Mitochondrial DNA Working with extremely degraded
More informationChapter 8: Recombinant DNA 2002 by W. H. Freeman and Company Chapter 8: Recombinant DNA 2002 by W. H. Freeman and Company
Genetic engineering: humans Gene replacement therapy or gene therapy Many technical and ethical issues implications for gene pool for germ-line gene therapy what traits constitute disease rather than just
More informationLarge-scale Research Data Management and Analysis Using Globus Services. Ravi Madduri Argonne National Lab University of Chicago @madduri
Large-scale Research Data Management and Analysis Using Globus Services Ravi Madduri Argonne National Lab University of Chicago @madduri Outline Who we are Challenges in Big Data Management and Analysis
More informationApplication Guide... 2
Protocol for GenomePlex Whole Genome Amplification from Formalin-Fixed Parrafin-Embedded (FFPE) tissue Application Guide... 2 I. Description... 2 II. Product Components... 2 III. Materials to be Supplied
More informationGene Mapping Techniques
Gene Mapping Techniques OBJECTIVES By the end of this session the student should be able to: Define genetic linkage and recombinant frequency State how genetic distance may be estimated State how restriction
More informationIntegrated Rule-based Data Management System for Genome Sequencing Data
Integrated Rule-based Data Management System for Genome Sequencing Data A Research Data Management (RDM) Green Shoots Pilots Project Report by Michael Mueller, Simon Burbidge, Steven Lawlor and Jorge Ferrer
More informationIllumina Sequencing Technology
Illumina Sequencing Technology Highest data accuracy, simple workflow, and a broad range of applications. Introduction Figure 1: Illumina Flow Cell Illumina sequencing technology leverages clonal array
More information