Introduction to NGS Analysis Tools

Size: px
Start display at page:

Download "Introduction to NGS Analysis Tools"

Transcription

1 National Center for Emerging and Zoonotic Infectious Diseases Introduction to NGS Analysis Tools Heather Carleton, PhD, MPH Team Lead, Enteric Diseases Bioinformatics, Enteric Diseases Laboratory Branch, DFWED, NCEZID, CDC Next Generation Sequencing: From concept to reality at public health laboratories June 6 th, 2016 Objectives Provide a basic overview of terminology surrounding next generation sequencing data Discuss analysis terminology Highlight NGS analysis tools Command line freely available tools On line/cloud based tools Commercially available analysis tools Discuss advantages/disadvantages to the tools 1

2 Why do you need analysis tools: To translate WGS data Consolidation of multiple workflows in the laboratory: Identification serotyping virulence profiling antimicrobial resistance characterization subtyping Analysis Tools Assembly (de novo) whole genome MLST Analysis Functional analysis (ANI, Serotype, antimicrobial resistance profile, annotation) Sequence QC Read mapping Reference-based assembly hqsnp analysis kmer (raw read/assembly) SNP analysis wgmlst analysis 2

3 What is a analysis/bioinformatics pipeline? QC de novo assembly wgmlst phylogenetic tree Pipeline refers to the series of tools used to go from raw sequence data to answer Types of analysis pipelines Bioinformatics Experience Freely available command-line/ on-line cloud-based/fee for service Commercial software 3

4 How to pick an analysis pipeline(s) Pick the tool that fits your users If you do not have bioinformaticians in your lab than using command line tools will be a challenge Make sure the tool delivers the output you need if you need a phylogenetic tree then it needs to do read mapping, snp detection, and phylogenetic inference Must provide quality checks of raw sequence data and analysis steps so you can evaluate success of tool Analysis Tools Sequen ce QC Assembly (de novo) whole genome MLST Analysis Functional analysis (ANI, Serotype, antimicrobial resistance profile, annotation) 4

5 Basic QC analysis Tools used to analyze the basic quality of a sequencing run or reads generated per isolate of a sequencing run FastQC (also available in BaseSpace) Torrent Server Geneious Qiagen/CLC workbench BioNumerics v7 Sequence QC Q score 95% Q30 Quality scores likelihood the base call is correct Phred part of fastq file generated from sequencer that scores base call quality Q30 the percentage of base calls that have a 1 in 1000 chance or less of being incorrect (Q20 1 incorrect in 100 base calls) indicates whether a base call is trustworthy and can be used in a hqsnp analysis 5

6 Sequence QC Read trimming Assess quality over the entire read by looking at quality score by base position and % GC by base position Most NGS machines have read trimming as part of machine workflow to remove indices and adaptors Sequence Quality Insert size Insert size refers to the length of the piece of DNA you are sequencing Generally want insert size to be larger than sequencing chemistry (i.e. if doing 2x250/500 cycle sequencing want insert size larger than 500bp) Bad insert size 2x150 sequencing Good insert size 6

7 Sequence QC Coverage Coverage at 40x Coverage at 5x NGS generates 100,000 or more reads per one genome sequenced Any single location on the genome can have zero to hundreds of sequence reads that cover the one region Sequence Analysis De Novo Assembly Assemble raw sequence data from ~100k reads to contigs Assemblers use different algorithms and are built to work with a specific NGS machine SPAdes, Velvet, Newbler BaseSpace/SPAdes plug in Torrent Server Geneious Qiagen/CLC workbench BioNumerics v7 7

8 Sequence Analysis De novo assembly Combine overlapping reads into a single contig Sequence Analysis de novo assembly quality Assembly metrics can indicate sequence quality Number of contigs raw reads assembles into Good: E. coli <200, Salmonella < 100, Listeria < 30 N50 statistic Calculated by summarizing the lengths of the biggest contigs until you reach 50% of total combined contig length Good: >200,000 bp 3 Million base pair genome (determined by sum of contig lengths) 750,000bp 500,000bp 350,000bp *N50 is 350,000 bp Indicates 1.5 Million base pairs, or cutoff for 50% combined contig length (N50) 8

9 Sequence Analysis Multi locus sequence typing Locus can be a gene or part of a gene any change (single nucleotide polymorphism, insertion, deletion, small inversion) is a new allele number Loci can cover the whole genome of an isolate, the core (in common) genes of a species, or house keeping genes of a genus (traditional MLST) cgmlst hq SNP Sequence Analysis MLST Comparing number (character) differences between isolates Requires an already developed scheme for the analyzed organism NCBI Pathogen pipeline (in development) BigsDB ( Ridom/SeqSphere ( BioNumerics v7 9

10 Sequence analysis functional annotation Predict isolate characteristics from WGS data (genus/species, serotype, antimicrobial resistance, virulence, etc.) NCBI Pathogen pipeline (antimicrobial resistance) Center for Genomic Epidemiology (CGE) (virulence, STEC/ Salmonella serotype, antimicrobial resistance) BioNumerics v7 (genus/species (ANIm), virulence, STEC/Salmonella serotype, antimicrobial resistance) Identifying Genus and Species from WGS data Can use databases MLST, ribosomal MLST, 16S to identify Genus and occasionally to species level Can use WGS methods similar to classic laboratory methods for identification, DNA DNA hybridization, to calculate Average Nucleotide Identity (ANI) between a query genome and a reference genome E. coli ACTAGAGGGAAA S. enterica GCATCCCCCGTT GCATCCCCCGTA query genome ANI score 98% for S.enterica 10

11 Inferring serotype from WGS Since the genes that code the O and H antigens and determine serotype are known can build a database that translates sequence to serotype Limitations Sometimes genes are not expressed (non motile isolates) There may be modifications to the antigen protein that are not encoded in the genes that originally make the protein Virulence factors from WGS data Virulence factors like Shiga toxin or other enterotoxins that are traditionally detected by serology, PCR, or real time PCR can be detected in WGS data using databases Publically available resources like the Center of Genomic Epidemiology VirulenceFinder can be used to find virulence genes in E. coli, Enterococcus, and S. aureus 11

12 Predicting antimicrobial resistance from WGS Acquired resistance Usually resistance genes (200bp 1,000bp) Highly conserved even between different genera (>98% identity) Usually located on mobile elements (plasmids, integrons, islands) Methods to detect assembled sequence, resistance databases (Resfinder, ARG ANNOT, FDA/NCBI AR database) Acquired Resistance Genes associated with a particular AR phenotype Phenotype Ampicillin Amoxicillin/ clavulanic acid Cefoxitin Ceftriaxone Ceftiofur Kanamycin Gentamicin Streptomycin Chloramphenicol Sulfisoxazole Trimethoprim/ sulphamethoxazole Tetracycline Genotype bla cmy 2 aph(3 ) Ia aac(3) VIa aada2, strab flor sul1, sul2 dfra12, sul1, sul2 teta 12

13 Predicting antimicrobial resistance from WGS Mutational resistance Usually SNPs, but can be insertions/deletions Usually chromosomal Genera or species specific Methods no available databases assembled sequence, in silico PCR raw reads, SNP analysis Analysis Tools Reference-based assembly Sequen ce QC Read mapping hqsnp analysis Functional analysis (ANI, Serotype, antimicrobial resistance profile, annotation) 13

14 Sequence Analysis Read mapping/ hqsnp analysis Map raw sequence data to a known reference genome Pick mapper based on sequencing chemistry and organism (diploid/haploid) Mapping used for downstream analysis including hqsnp samtools, bowtie2, smalt (can wrap some of these in Galaxy) BaseSpace (bacterial, viral, human, and cancer variant apps), torrent server NCBI pathogen pipeline BioNumerics v7, CLC Genome workbench, Geneious Sequence Analysis high quality single nucleotide polymorphisms (hqsnps) Sequence Reads Sequence reads Sequence reads What makes a SNP high quality (hq)? Apply a quality filter that filters out nucleotides in sequence reads for comparison based on sequence coverage, quality, location Quality filtered Sequence Reads ready for analysis 14

15 What to call a SNP SNPs called based on: Quality Coverage Base frequency The differences between the reference and compared genome are extracted and used to determine relatedness ATGTTACTC ATGTTCCTC ATGTTCCTC ATGTTCCTC ATGTTCCTC ATGTTCCTC ATGTTTCTC ATGTTCCTC ATGTTCCTC ATGTTCCTC ATGTTGCTC ATGTTCCTC ATGTTCCTC ATGTTCCTC ATGTTGCTC reference Is it a SNP? Where to call a SNP? Mobile elements genes Raw reads Mask mobile elements -do no consider SNPs in this location Only call SNPs in genes Not all SNP pipelines are equal where you call SNPs will affect the total SNP count SNPs relevant for phylogenetic analysis are vertically transmitted, not horizontally, so horizontal genetic elements like phages can be masked 15

16 Where to call a SNP pick the right reference Choice of reference genome affects analysis more closely related reference more likely to identify true SNP differences How to interpret hqsnps phylogenetic trees Use the differences you identified by hqsnp to infer the relatedness or phylogeny of isolates actgaatta 3 ggagaatta 1 ggataatta 1 1 ggattatta ggagagtta 6 Isolate C Isolate A ggatccccc Isolate B 5 actgccggt Isolate D genetic change 16

17 NCBI Pathogen Detection Pipeline NCBI Submission Portal BioProject BioSamples SRA GenBank NCBI Pathogen Pipeline QC Kmer analysis Genome Assembly Genome Annotation Genome Placement Clustering SNP analysis Tree Construction Reports Automated Bacterial Assembly Reference Distance tree SRA Reads sample 1 Trim reads (Ns, adaptor) Find closest reference genome(s) De novo assembly panel Argo (Reference assisted assembly) SOAP denovo MaSuRCA SPAdes GS-assembler (newbler) Celera Assembler ArgoCA (Combined Assembly) Reads remapped to combined assembly Contig fasta Read placements (bam) Quality profile 17

18 Results Available Now NCBI Pathogen Detection SNP Pipeline: example 1 - stone fruit outbreak 18

19 CDC SNP extraction tool Lyve SET Developed for analysis of raw sequence data from foodborne pathogens Works with both ion torrent and illumina data (need to use 2 different mappers Can filter based on quality and clustered SNPs and filter out phages automatically SET Clean raw reads cg-pipeline Map reads to reference SMALT Identify SNPs Varscan Create phylogeny RaxML SNP matrix pairwise differences phylogenetic tree FDA SNP pipeline SNP pipeline Developed for analysis of sequence data for foodborne pathogens Excellent documentation online pipeline.readthedocs.io/en/latest/ Biostatistics/snp pipeline Map reads to reference Bowtie2 Identify SNPs Varscan SNP matrix pairwise differences Output for phylogenetic analysis 19

20 Analysis Tools Sequence QC kmer (raw read based/assembly) SNP analysis wgmlst analysis Sequence analysis reference free raw read and assembly based approaches Analysis does not require a reference Can use kmer based analyses to measure relatedness between isolates Can also use to fast match against a known allele/reference ksnp ( MASH NCBI pathogen pipeline (kmer tree) Center for genomic epidemiology CLC genome workbench BioNumerics v7.5 wgmlst 20

21 Kmer based analysis Computer algorithms use a sliding window to chop up sequence reads into shorter lengths (k) of DNA kmers kmers are compared to identify differences Read (15bp) ACTGAACTGACTCAA ACTGAACTGACTCAC K-mer (10bp) ACTGAACTGA CTGAACTGAC TGAACTGACT AACTGACTCA ACTGACTCAA Identical K-mers Unique K-mer ACTGAACTGA CTGAACTGAC TGAACTGACT AACTGACTCA ACTGACTCAC Isolate 1 Isolate 2 KSNP based analysis Computer algorithms use a sliding window to chop up sequence reads into shorter lengths (k) of DNA k is always an odd number Raw Read (15bp) Compare base pair differences at central position of kmer ACTGAACTGACTCAA ACTGCACTGACTCAA K-mer (9bp) ACTGAACTG CTGAACTGA TGAACTGAC AACTGACTC ACTGACTCA ACTGCACTG CTGCACTGA TGCACTGAC CACTGACTC ACTGACTCA Isolate 1 Isolate 2 21

22 Kmer analysis identifying organisms End to End Analysis Tools Assembly (de novo) whole genome MLST Analysis Functional analysis (ANI, Serotype, antimicrobial resistance profile, annotation) Sequence QC Read mapping Reference-based assembly hqsnp analysis kmer (raw read/assembly) SNP analysis wgmlst analysis 22

23 Tools that offer end to end solutions: BioNumerics v7.6 Tools for QC, assembly, wgmlst, hqsnp, functional prediction in each single button workflows Functions as a database so the metadata needed to interpret the analysis is easily viewable For bacteriology, virology, mycology, animals, and plants Tools that offer end to end solutions: CLC Genomics Has tools to handle haploid and diploid genomes Nice graphics and reporting features Can export workflows for others to use 23

24 Tools that offer end to end solutions: Illumina BaseSpace Conclusions: Pick the tool that fits your need Think about whether you will be doing CLIA or CAP certified tests through the pipeline and what kind of control and customization you need Make sure your laboratorians can use the tool and interpret the output 24

25 Questions? Use of trade names is for identification only and does not imply endorsement by the Centers for Disease Control and Prevention or the U.S. Department of Health and Human Services. For more information, contact CDC CDC INFO ( ) TTY: The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention. Resources: Program What for? Where to find it Cost? Platform BioNumerics 7.5 CLC Bio Genomics Workbench Geneious Assembly, wgmlst, SNP analysis Workflows, read metrics, assemblies, etc, SNP analyses Assemblies, trees, SNP analysis Yes Yes Windows Windows/ Linux Yes Windows MEGA6 Phylogenies megasoftware.net/ No Windows Lasergene Assemblies, read metrics, Yes Windows analysis NCBI Genome Workbench CFSAN SNP pipeline Snp Extraction Tool Viewing trees, analysis Assembly, read metrics, assembly metrics, read cleaning, etc Read cleaning, Creating Phylogenies ools/gbench/ atics.com/products/clcgenomics-workbench/ sourceforge.net/projects/cgpipeline No No Windows/ Linux Linux github.com/lskatz/lyve-set No Linux 25

The Basics of Understanding Whole Genome Next Generation Sequence Data

The Basics of Understanding Whole Genome Next Generation Sequence Data The Basics of Understanding Whole Genome Next Generation Sequence Data Heather Carleton-Romer, MPH, Ph.D. ASM-CDC Infectious Disease and Public Health Microbiology Postdoctoral Fellow PulseNet USA Next

More information

The Basics of Understanding Whole Genome Next Generation Sequence Data

The Basics of Understanding Whole Genome Next Generation Sequence Data The Basics of Understanding Whole Genome Next Generation Sequence Data Heather Carleton, MPH, Ph.D. ASM-CDC Infectious Disease and Public Health Microbiology Postdoctoral Fellow PulseNet USA Next Generation

More information

Introduction to PulseNet WGS Tools in BioNumerics v7.6

Introduction to PulseNet WGS Tools in BioNumerics v7.6 National Center for Emerging and Zoonotic Infectious Diseases Introduction to PulseNet WGS Tools in BioNumerics v7.6 Steven Stroika PulseNet CDC PulseNet/OutbreakNet Regional Meeting February 2019 Overview

More information

Developing Tools for Rapid and Accurate Post-Sequencing Analysis of Foodborne Pathogens. Mitchell Holland, Noblis

Developing Tools for Rapid and Accurate Post-Sequencing Analysis of Foodborne Pathogens. Mitchell Holland, Noblis Developing Tools for Rapid and Accurate Post-Sequencing Analysis of Foodborne Pathogens Mitchell Holland, Noblis Agenda Introduction Whole Genome Sequencing Analysis Pipeline Sequence Alignment SNPs and

More information

Beef Industry Safety Summit Renaissance Austin Hotel 9721 Arboretum Blvd. Austin, TX March 1-3

Beef Industry Safety Summit Renaissance Austin Hotel 9721 Arboretum Blvd. Austin, TX March 1-3 1 USDA, Food Safety and Inspection Service Beef Industry Safety Summit - 2016 Renaissance Austin Hotel 9721 Arboretum Blvd. Austin, TX 78759 March 1-3 Uday Dessai MPH, MS, PhD Senior Public Health Advisor

More information

Validating Bionumerics 7.6: A strategic approach from Oregon

Validating Bionumerics 7.6: A strategic approach from Oregon Validating Bionumerics 7.6: A strategic approach from Oregon Karim Morey, MS, M(ASCP) Oregon State Public Health Laboratory PulseNet West Coast Regional Meeting February 2019 Outline Compliance requirements

More information

Whole Genome Sequence Data Quality Control and Validation

Whole Genome Sequence Data Quality Control and Validation Whole Genome Sequence Data Quality Control and Validation GoSeqIt ApS / Ved Klædebo 9 / 2970 Hørsholm VAT No. DK37842524 / Phone +45 26 97 90 82 / Web: www.goseqit.com / mail: mail@goseqit.com Table of

More information

Introduction to CGE tools

Introduction to CGE tools Introduction to CGE tools Pimlapas Leekitcharoenphon (Shinny) Research Group of Genomic Epidemiology, DTU-Food. WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics.

More information

Canada's IRIDA platform for genomic epidemiology. Gary Van Domselaar Chief, Bioinformatics National Microbiology Lab Public Health Agency of Canada

Canada's IRIDA platform for genomic epidemiology. Gary Van Domselaar Chief, Bioinformatics National Microbiology Lab Public Health Agency of Canada Canada's IRIDA platform for genomic epidemiology Gary Van Domselaar Chief, Bioinformatics National Microbiology Lab Public Health Agency of Canada Integrated Rapid Infectious Disease Analysis informatics

More information

CDC s Advanced Molecular Detection (AMD) Sequence Data Analysis and Management

CDC s Advanced Molecular Detection (AMD) Sequence Data Analysis and Management CDC s Advanced Molecular Detection (AMD) Sequence Data Analysis and Management Scott Sammons Technology Officer Office of Advanced Molecular Detection National Center for Emerging and Zoonotic Infectious

More information

Bioinformatics- Data Analysis

Bioinformatics- Data Analysis Bioinformatics- Data Analysis Erin H. Graf, PhD, D(ABMM) Infectious Disease Diagnostics Laboratory, Children s Hospital of Philadelphia Department of Pathology and Laboratory Medicine, University of Pennsylvania

More information

Detecting Clusters and Reporting Results

Detecting Clusters and Reporting Results National Center for Emerging and Zoonotic Infectious Diseases Detecting Clusters and Reporting Results Beth Tolar Salmonella Database Coordinator PulseNet Central Regional Meeting March 2019 Update to

More information

Current status of universal whole genome sequencing of Mycobacterium tuberculosis in the United States

Current status of universal whole genome sequencing of Mycobacterium tuberculosis in the United States Current status of universal whole genome sequencing of Mycobacterium tuberculosis in the United States Lauren Cowan, PhD Medical Consultant Meeting San Antonio, TX November 29-30, 2018 1 EXCELLENCE EXPERTISE

More information

The implementation and application of Whole Genome Sequencing in the Campylobacter Reference Laboratory at Public Health England Craig Swift

The implementation and application of Whole Genome Sequencing in the Campylobacter Reference Laboratory at Public Health England Craig Swift The implementation and application of Whole Genome Sequencing in the Campylobacter Reference Laboratory at Public Health England Craig Swift Campylobacter EURL workshop (2018) The Gastrointestinal Bacteria

More information

Rue Juliette Wytsmanstraat Brussels Belgium T F

Rue Juliette Wytsmanstraat Brussels Belgium T F Kevin Vanneste, PhD Bioinformatics Platform Platform Biotechnology and Molecular Biology Department Expertise, Service Provision and Customer Relations Collaboration between the EURL-VTEC and the Platform

More information

Updates from CDC: Cluster Detection and Reporting Guidelines

Updates from CDC: Cluster Detection and Reporting Guidelines National Center for Emerging and Zoonotic Infectious Diseases Updates from CDC: Cluster Detection and Reporting Guidelines Molly Leeper Salmonella Database Manager PulseNet Western Regional Meeting February

More information

VTEC strains typing: from traditional methods to NGS

VTEC strains typing: from traditional methods to NGS VTEC strains typing: from traditional methods to NGS 2 nd course on bioinformatics tools for Next Generation Sequencing data mining: use of bioinformatics tools for typing pathogenic E. coli ISS, Rome

More information

Bioinformatics Tools and Pipelines for Real-Time Pathogen Surveillance

Bioinformatics Tools and Pipelines for Real-Time Pathogen Surveillance Bioinformatics Tools and Pipelines for Real-Time Pathogen Surveillance Errol Strain, Ph.D. Chief, Biostatistics Branch FDA/OFVM/CFSAN/OAO/DPHIA 3/24/2014 Overview 1. Validation and Proficiency Testing

More information

Computational assembly for prokaryotic sequencing projects

Computational assembly for prokaryotic sequencing projects Computational assembly for prokaryotic sequencing projects Lee Katz, Ph.D. Bioinformatician, Enteric Diseases Laboratory Branch (EDLB) Enteric Diseases Bioinformatics Team (EDBiT) January 30, 2017 Disclaimers

More information

Whole-Genome Sequencing (WGS) for Food Safety

Whole-Genome Sequencing (WGS) for Food Safety Whole-Genome Sequencing (WGS) for Food Safety Errol Strain, Ph.D. Director, Biostatistics and Bioinformatics Staff Center for Food Safety and Applied Nutrition U.S. Food Drug Administration IFSH Meeting

More information

From Bands to Base Pairs: Implementation of WGS in a PulseNet Laboratory

From Bands to Base Pairs: Implementation of WGS in a PulseNet Laboratory From Bands to Base Pairs: Implementation of WGS in a PulseNet Laboratory Sara Wagner Microbiologist WI State Lab of Hygiene InFORM Meeting Nov 19, 2015 Objectives Describe WGS implementation at WSLH What

More information

EURL WORKING GROUP ON WHOLE GENOME SEQUENCING AND PULSENET INTERNATIONAL

EURL WORKING GROUP ON WHOLE GENOME SEQUENCING AND PULSENET INTERNATIONAL EURL WORKING GROUP ON WHOLE GENOME SEQUENCING AND PULSENET INTERNATIONAL EURL-Campylobacter workshop, 9/10-2018 Joakim Skarin, SVA Objectives of the WG-NGS To promote the use of NGS across the EURL networks

More information

CGE Pipeline. Content 1. The Batch Upload 2. The Pipeline 3. The User System 4. The List Tool 5. The Map Tool 6. Exercises

CGE Pipeline. Content 1. The Batch Upload 2. The Pipeline 3. The User System 4. The List Tool 5. The Map Tool 6. Exercises CGE Pipeline Content 1. The Batch Upload 2. The Pipeline 3. The User System 4. The List Tool 5. The Map Tool 6. Exercises Jose Luis Bellod Cisneros PhD. Student Content 1. The Batch Upload 2. The Pipeline

More information

Whole Genome Sequencing for Enteric Pathogen Surveillance and Outbreak Investigations

Whole Genome Sequencing for Enteric Pathogen Surveillance and Outbreak Investigations Whole Genome Sequencing for Enteric Pathogen Surveillance and Outbreak Investigations Anne Maki, Manager, Enteric, Environmental, Molecular Surveillance and Bacterial Sexually Transmitted Infections, Public

More information

Data Intensive Biomedical Research: The EU RL VTEC efforts to take up the NGS challenge. EU RL for E. coli Annual Workshop 2015

Data Intensive Biomedical Research: The EU RL VTEC efforts to take up the NGS challenge. EU RL for E. coli Annual Workshop 2015 Data Intensive Biomedical Research: The EU RL VTEC efforts to take up the NGS challenge EU RL for E. coli Annual Workshop 2015 NGS adoption: Worldwide Source: Omicsmap.com November, 2015 Data Production

More information

CGE Pipeline. Content 1. The User System 2. The Batch Upload 3. The Pipeline 4. The List Tool 5. The Map Tool 6. FuturePlans 7.

CGE Pipeline. Content 1. The User System 2. The Batch Upload 3. The Pipeline 4. The List Tool 5. The Map Tool 6. FuturePlans 7. CGE Pipeline Content 1. The User System 2. The Batch Upload 3. The Pipeline 4. The List Tool 5. The Map Tool 6. FuturePlans 7. Q&A Jose Luis Bellod Cisneros PhD. Student Content 1. The Batch Upload 2.

More information

Data Basics. Josef K Vogt Slides by: Simon Rasmussen Next Generation Sequencing Analysis

Data Basics. Josef K Vogt Slides by: Simon Rasmussen Next Generation Sequencing Analysis Data Basics Josef K Vogt Slides by: Simon Rasmussen 2017 Generalized NGS analysis Sample prep & Sequencing Data size Main data reductive steps SNPs, genes, regions Application Assembly: Compare Raw Pre-

More information

Using Galaxy for the analysis of NGS-derived pathogen genomes in clinical microbiology

Using Galaxy for the analysis of NGS-derived pathogen genomes in clinical microbiology Using Galaxy for the analysis of NGS-derived pathogen genomes in clinical microbiology Anthony Underwood*, Paul-Michael Agapow, Michel Doumith and Jonathan Green. Bioinformatics Unit, Health Protection

More information

SNP calling and VCF format

SNP calling and VCF format SNP calling and VCF format Laurent Falquet, Oct 12 SNP? What is this? A type of genetic variation, among others: Family of Single Nucleotide Aberrations Single Nucleotide Polymorphisms (SNPs) Single Nucleotide

More information

TECHNICAL REPORT. Fifth external quality assessment scheme for Listeria monocytogenes typing.

TECHNICAL REPORT. Fifth external quality assessment scheme for Listeria monocytogenes typing. TECHNICAL REPORT Fifth external quality assessment scheme for Listeria monocytogenes typing www.ecdc.europa.eu ECDC TECHNICAL REPORT Fifth external quality assessment scheme for Listeria monocytogenes

More information

Introduction to DNA-Sequencing

Introduction to DNA-Sequencing informatics.sydney.edu.au sih.info@sydney.edu.au The Sydney Informatics Hub provides support, training, and advice on research data, analyses and computing. Talk to us about your computing infrastructure,

More information

De Novo Assembly of High-throughput Short Read Sequences

De Novo Assembly of High-throughput Short Read Sequences De Novo Assembly of High-throughput Short Read Sequences Chuming Chen Center for Bioinformatics and Computational Biology (CBCB) University of Delaware NECC Third Skate Genome Annotation Workshop May 23,

More information

IFSH WHOLE GENOME SEQUENCING FOR FOOD INDUSTRY SYMPOSIUM May 22-23, 2017

IFSH WHOLE GENOME SEQUENCING FOR FOOD INDUSTRY SYMPOSIUM May 22-23, 2017 1 USDA, Food Safety and Inspection Service IFSH WHOLE GENOME SEQUENCING FOR FOOD INDUSTRY SYMPOSIUM May 22-23, 2017 Chicago Marriott Southwest at Burr Ridge 1200 Burr Ridge Parkway, Burr Ridge, IL 60527

More information

From classical molecular typing to WGS in a food safety context: WGS at EFSA

From classical molecular typing to WGS in a food safety context: WGS at EFSA From classical molecular typing to WGS in a food safety context: WGS at EFSA Beatriz Guerra EURL-AR WGS Training, Copenhage, Denmark, 27.09.17 WGS FOR FOOD SAFETY AT EFSA Molecular Typing Recent Past:

More information

Introductie en Toepassingen van Next-Generation Sequencing in de Klinische Virologie. Sander van Boheemen Medical Microbiology

Introductie en Toepassingen van Next-Generation Sequencing in de Klinische Virologie. Sander van Boheemen Medical Microbiology Introductie en Toepassingen van Next-Generation Sequencing in de Klinische Virologie Sander van Boheemen Medical Microbiology Next-generation sequencing Next-generation sequencing (NGS), also known as

More information

Whole Genome Sequencing for food safety FSA Chief Scientific Advisor Report and 2013 Listeria pilot study

Whole Genome Sequencing for food safety FSA Chief Scientific Advisor Report and 2013 Listeria pilot study Whole Genome Sequencing for food safety FSA Chief Scientific Advisor Report and 2013 Listeria pilot study Dr Edward Hayes Date: July 2016, Version 1 Foodborne Pathogens 280,000 cases of Campylobacter,

More information

Development and Implementation of a Quality System for Next-Generation Sequencing

Development and Implementation of a Quality System for Next-Generation Sequencing Development and Implementation of a Quality System for Next-Generation Sequencing Lauren Turner, PhD Lead Scientist Virginia Division of Consolidated Laboratory Services DCLS Phased Implementation of NGS

More information

Practical quality control for whole genome sequencing in clinical microbiology

Practical quality control for whole genome sequencing in clinical microbiology Practical quality control for whole genome sequencing in clinical microbiology John WA Rossen, PhD, MMM Department of Medical Microbiology, University of Groningen, UMCG, Groningen, The Netherlands Disclosure

More information

Bringing Whole Genome Sequencing on Board in a State Regulatory Laboratory

Bringing Whole Genome Sequencing on Board in a State Regulatory Laboratory Bringing Whole Genome Sequencing on Board in a State Regulatory Laboratory Brian D. Sauders, PhD NY State Dept. of Agriculture & Markets Food Laboratory The Food Laboratory! 2 Major laboratory sections:

More information

Analytics Behind Genomic Testing

Analytics Behind Genomic Testing A Quick Guide to the Analytics Behind Genomic Testing Elaine Gee, PhD Director, Bioinformatics ARUP Laboratories 1 Learning Objectives Catalogue various types of bioinformatics analyses that support clinical

More information

De novo whole genome assembly

De novo whole genome assembly De novo whole genome assembly Qi Sun Bioinformatics Facility Cornell University Sequencing platforms Short reads: o Illumina (150 bp, up to 300 bp) Long reads (>10kb): o PacBio SMRT; o Oxford Nanopore

More information

GENOME ASSEMBLY FINAL PIPELINE AND RESULTS

GENOME ASSEMBLY FINAL PIPELINE AND RESULTS GENOME ASSEMBLY FINAL PIPELINE AND RESULTS Faction 1 Yanxi Chen Carl Dyson Sean Lucking Chris Monaco Shashwat Deepali Nagar Jessica Rowell Ankit Srivastava Camila Medrano Trochez Venna Wang Seyed Alireza

More information

2014 APHL Next Generation Sequencing (NGS) Survey

2014 APHL Next Generation Sequencing (NGS) Survey APHL would like you to complete the Next Generation Sequencing (NGS) in Public Health Laboratories Survey. The purpose of this survey is to collect information on current capacities for NGS testing and

More information

GALAXY TRAKR FOR STATE PUBLIC HEALTH BIOINFORMATICS INTRODUCTORY TRAININGS, DATA ANALYTICS, & BIOINFORMATICS COLLABORATIONS

GALAXY TRAKR FOR STATE PUBLIC HEALTH BIOINFORMATICS INTRODUCTORY TRAININGS, DATA ANALYTICS, & BIOINFORMATICS COLLABORATIONS GALAXY TRAKR FOR STATE PUBLIC HEALTH BIOINFORMATICS INTRODUCTORY TRAININGS, DATA ANALYTICS, & BIOINFORMATICS COLLABORATIONS Kevin G. Libuit, M.S. Senior Informatics Scientist Division of Consolidated Laboratory

More information

Targeted Sequencing in the NBS Laboratory

Targeted Sequencing in the NBS Laboratory Targeted Sequencing in the NBS Laboratory Christopher Greene, PhD Newborn Screening and Molecular Biology Branch Division of Laboratory Sciences Gene Sequencing in Public Health Newborn Screening February

More information

Overview of CIDT Challenges and Opportunities

Overview of CIDT Challenges and Opportunities Overview of CIDT Challenges and Opportunities Peter Gerner-Smidt, MD, DSc Enteric Diseases Laboratory Branch InFORM II Phoenix, AZ, 19 November 2015 National Center for Emerging and Zoonotic Infectious

More information

ESCMID Online Lecture Library. by author

ESCMID Online Lecture Library. by author ESCMID WS Rapid NGS for Characterization and Typing of Resistant Gram-Negative Bacilli 7-9 October 2015 João André Carriço, Microbiology Institute and Instituto de Medicina Molecular, Faculty of Medicine,

More information

De Novo Assembly (Pseudomonas aeruginosa MAPO1 ) Sample to Insight

De Novo Assembly (Pseudomonas aeruginosa MAPO1 ) Sample to Insight De Novo Assembly (Pseudomonas aeruginosa MAPO1 ) Sample to Insight 1 Workflow Import NGS raw data QC on reads De novo assembly Trim reads Finding Genes BLAST Sample to Insight Case Study Pseudomonas aeruginosa

More information

New York State s experience with analyzing, interpreting, and sharing whole genome sequence data for surveillance of enteric organisms.

New York State s experience with analyzing, interpreting, and sharing whole genome sequence data for surveillance of enteric organisms. New York State s experience with analyzing, interpreting, and sharing whole genome sequence data for surveillance of enteric organisms. InForm 11/18/15 William Wolfgang, PhD Wadsworth Center, NYSDOH william.wolfgang@health.ny.gov

More information

NGS in Pathology Webinar

NGS in Pathology Webinar NGS in Pathology Webinar NGS Data Analysis March 10 2016 1 Topics for today s presentation 2 Introduction Next Generation Sequencing (NGS) is becoming a common and versatile tool for biological and medical

More information

Illumina Sequencing Error Profiles and Quality Control

Illumina Sequencing Error Profiles and Quality Control Illumina Sequencing Error Profiles and Quality Control RNA-seq Workflow Biological samples/library preparation Sequence reads FASTQC Adapter Trimming (Optional) Splice-aware mapping to genome Counting

More information

Experimental Design. Sequencing. Data Quality Control. Read mapping. Differential Expression analysis

Experimental Design. Sequencing. Data Quality Control. Read mapping. Differential Expression analysis -Seq Analysis Quality Control checks Reproducibility Reliability -seq vs Microarray Higher sensitivity and dynamic range Lower technical variation Available for all species Novel transcript identification

More information

Challenges and opportunities for whole genome sequencing based surveillance of antibiotic resistance

Challenges and opportunities for whole genome sequencing based surveillance of antibiotic resistance Challenges and opportunities for whole genome sequencing based surveillance of antibiotic resistance Prof. Willem van Schaik Professor in Microbiology and Infection Institute of Microbiology and Infection

More information

Fast, Accurate and Sensitive DNA Variant Detection from Sanger Sequencing:

Fast, Accurate and Sensitive DNA Variant Detection from Sanger Sequencing: Fast, Accurate and Sensitive DNA Variant Detection from Sanger Sequencing: Patented, Anti-Correlation Technology Provides 99.5% Accuracy & Sensitivity to 5% Variant Knowledge Base and External Annotation

More information

C3BI. VARIANTS CALLING November Pierre Lechat Stéphane Descorps-Declère

C3BI. VARIANTS CALLING November Pierre Lechat Stéphane Descorps-Declère C3BI VARIANTS CALLING November 2016 Pierre Lechat Stéphane Descorps-Declère General Workflow (GATK) software websites software bwa picard samtools GATK IGV tablet vcftools website http://bio-bwa.sourceforge.net/

More information

Genomic epidemiology of bacterial pathogens. Sylvain BRISSE Microbial Evolutionary Genomics, Institut Pasteur, Paris

Genomic epidemiology of bacterial pathogens. Sylvain BRISSE Microbial Evolutionary Genomics, Institut Pasteur, Paris Genomic epidemiology of bacterial pathogens Sylvain BRISSE Microbial Evolutionary Genomics, Institut Pasteur, Paris Typing Population genetics Analysis of strain diversity within species Aim: Local epidemiology?

More information

Subtyping the top 30 Salmonella serotypes using a combination of CRISPR elements and virulence genes: Salmonella CRISPR-MLVST

Subtyping the top 30 Salmonella serotypes using a combination of CRISPR elements and virulence genes: Salmonella CRISPR-MLVST Subtyping the top 30 Salmonella serotypes using a combination of CRISPR elements and virulence genes: Salmonella CRISPR-MLVST Heather Carleton, MPH, Ph.D. InFORM 2013 National Center for Emerging and Zoonotic

More information

A year in clinical bioinformatics

A year in clinical bioinformatics Division of Clinical Microbiology A year in clinical bioinformatics Helena Seth-Smith, PhD October 2018 ICCMg " the application of next generation sequencing to clinical samples in order to recover information

More information

Whole genome sequencing in the reference laboratory: An Introduction & Overview

Whole genome sequencing in the reference laboratory: An Introduction & Overview Whole genome sequencing in the reference laboratory: An Introduction & Overview 1 WGS Services in Scotland STEC reference service Salmonella & Shigella reference services.only the beginning! 2 Typing -

More information

Next generation sequencing in diagnostic laboratories: opportunities and challenges

Next generation sequencing in diagnostic laboratories: opportunities and challenges Next generation sequencing in diagnostic laboratories: opportunities and challenges Vitali Sintchenko Marie Bashir Institute for Emerging Infectious Diseases & Biosecurity Declaration No conflict of interest

More information

Transcriptomics analysis with RNA seq: an overview Frederik Coppens

Transcriptomics analysis with RNA seq: an overview Frederik Coppens Transcriptomics analysis with RNA seq: an overview Frederik Coppens Platforms Applications Analysis Quantification RNA content Platforms Platforms Short (few hundred bases) Long reads (multiple kilobases)

More information

Sanger vs Next-Gen Sequencing

Sanger vs Next-Gen Sequencing Tools and Algorithms in Bioinformatics GCBA815/MCGB815/BMI815, Fall 2017 Week-8: Next-Gen Sequencing RNA-seq Data Analysis Babu Guda, Ph.D. Professor, Genetics, Cell Biology & Anatomy Director, Bioinformatics

More information

Introduction to RNA sequencing

Introduction to RNA sequencing Introduction to RNA sequencing Bioinformatics perspective Olga Dethlefsen NBIS, National Bioinformatics Infrastructure Sweden November 2017 Olga (NBIS) RNA-seq November 2017 1 / 49 Outline Why sequence

More information

Introduction to Whole Genome Sequencing and its Applications in Microbial Diagnostics

Introduction to Whole Genome Sequencing and its Applications in Microbial Diagnostics Introduction to Whole Genome Sequencing and its Applications in Microbial Diagnostics Workshop on Whole Genome Sequencing and Analysis, 19-21 Mar. 2018 Whole genome sequencing is currently revolutionising

More information

Introduction to the MiSeq

Introduction to the MiSeq Introduction to the MiSeq 2011 Illumina, Inc. All rights reserved. Illumina, illuminadx, BeadArray, BeadXpress, cbot, CSPro, DASL, Eco, Genetic Energy, GAIIx, Genome Analyzer, GenomeStudio, GoldenGate,

More information

Bionano Access : Assembly Report Guidelines

Bionano Access : Assembly Report Guidelines Bionano Access : Assembly Report Guidelines Document Number: 30255 Document Revision: A For Research Use Only. Not for use in diagnostic procedures. Copyright 2018 Bionano Genomics Inc. All Rights Reserved

More information

From Infection to Genbank

From Infection to Genbank From Infection to Genbank How a pathogenic bacterium gets its genome to NCBI Torsten Seemann VLSCI - Life Sciences Computation Centre - Genomics Theme - Lab Meeting - Friday 27 April 2012 The steps 1.

More information

Starting Bioinformatics from Zero as a Biologist

Starting Bioinformatics from Zero as a Biologist Starting Bioinformatics from Zero as a Biologist Presented by Jessica Chen, Andrea (Ray) Etter, Peter Cook Sponsored by IEH Laboratories & Consulting Organized by the Developing Food Safety Professionals

More information

Whole genome and core genome multilocus sequence typing and single nucleotide

Whole genome and core genome multilocus sequence typing and single nucleotide AEM Accepted Manuscript Posted Online 26 May 2017 Appl. Environ. Microbiol. doi:10.1128/aem.00633-17 Copyright 2017 Chen et al. This is an open-access article distributed under the terms of the Creative

More information

From Variants to Pathways: Agilent GeneSpring GX s Variant Analysis Workflow

From Variants to Pathways: Agilent GeneSpring GX s Variant Analysis Workflow From Variants to Pathways: Agilent GeneSpring GX s Variant Analysis Workflow Technical Overview Import VCF Introduction Next-generation sequencing (NGS) studies have created unanticipated challenges with

More information

DNA concentration and purity were initially measured by NanoDrop 2000 and verified on Qubit 2.0 Fluorometer.

DNA concentration and purity were initially measured by NanoDrop 2000 and verified on Qubit 2.0 Fluorometer. DNA Preparation and QC Extraction DNA was extracted from whole blood or flash frozen post-mortem tissue using a DNA mini kit (QIAmp #51104 and QIAmp#51404, respectively) following the manufacturer s recommendations.

More information

Introduction to Whole Genome Sequencing and its Applications in Microbial Diagnostics

Introduction to Whole Genome Sequencing and its Applications in Microbial Diagnostics Introduction to Whole Genome Sequencing and its Applications in Microbial Diagnostics Workshop on Whole Genome Sequencing and Analysis, 27-29 Mar. 2017 Whole genome sequencing is currently revolutionising

More information

Introduction to Whole Genome Sequencing and its Applications in Microbial Diagnostics

Introduction to Whole Genome Sequencing and its Applications in Microbial Diagnostics Introduction to Whole Genome Sequencing and its Applications in Microbial Diagnostics Workshop on Whole Genome Sequencing and Analysis, 2-4 Oct. 2017 Whole genome sequencing is currently revolutionising

More information

Antisera QC and IQCP and Associated Challenges

Antisera QC and IQCP and Associated Challenges Antisera QC and IQCP and Associated Challenges Patti Fields Enteric Diseases Laboratory Branch (EDLB) CDC 2017 APHL Annual Meeting Providence, Rhode Island June 14, 2017 National Center for Emerging and

More information

by author Bacterial typing - what methodology should I use? MTE Session ECCMID 2017 VIENNA, 25 APRIL 2017 L u í s a V i e i ra P e i xe

by author Bacterial typing - what methodology should I use? MTE Session ECCMID 2017 VIENNA, 25 APRIL 2017 L u í s a V i e i ra P e i xe Bacterial typing - what methodology should I use? MTE Session ECCMID 2017 VIENNA, 25 APRIL 2017 L u í s a V i e i ra P e i xe U C I B I O @ R E Q U I M T E, F a c u l t y o f P h a r m a c y U n i v e

More information

Verocytotoxin producing Escherichia coli (VTEC) diagnostics

Verocytotoxin producing Escherichia coli (VTEC) diagnostics Verocytotoxin producing Escherichia coli (VTEC) diagnostics Workshop on Whole Genome Sequencing and Analysis, 27-29 Mar. 2017 Learning objective: After this lecture and exercise, you should be able to

More information

Setting the Course: Virginia's experience navigating information technology and bioinformatics needs for whole genome sequencing

Setting the Course: Virginia's experience navigating information technology and bioinformatics needs for whole genome sequencing Setting the Course: Virginia's experience navigating information technology and bioinformatics needs for whole genome sequencing Lauren Turner, Ph.D. Virginia Division of Consolidated Laboratory Services

More information

WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare?

WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare? Pathogens 2014, 3, 437-458; doi:10.3390/pathogens3020437 Review OPEN ACCESS pathogens ISSN 2076-0817 www.mdpi.com/journal/pathogens WGS Analysis and Interpretation in Clinical and Public Health Microbiology

More information

Next Gen Sequencing. Expansion of sequencing technology. Contents

Next Gen Sequencing. Expansion of sequencing technology. Contents Next Gen Sequencing Contents 1 Expansion of sequencing technology 2 The Next Generation of Sequencing: High-Throughput Technologies 3 High Throughput Sequencing Applied to Genome Sequencing (TEDed CC BY-NC-ND

More information

Genome 373: Mapping Short Sequence Reads II. Doug Fowler

Genome 373: Mapping Short Sequence Reads II. Doug Fowler Genome 373: Mapping Short Sequence Reads II Doug Fowler The final Will be in this room on June 6 th at 8:30a Will be focused on the second half of the course, but will include material from the first half

More information

Verocytotoxin producing Escherichia coli (VTEC) diagnostics

Verocytotoxin producing Escherichia coli (VTEC) diagnostics Verocytotoxin producing Escherichia coli (VTEC) diagnostics Workshop on Whole Genome Sequencing and Analysis, 2-4 Oct. 2017 Learning objective: After this lecture and exercise, you should be able to describe

More information

Genome Assembly Software for Different Technology Platforms. PacBio Canu Falcon. Illumina Soap Denovo Discovar Platinus MaSuRCA.

Genome Assembly Software for Different Technology Platforms. PacBio Canu Falcon. Illumina Soap Denovo Discovar Platinus MaSuRCA. Genome Assembly Software for Different Technology Platforms PacBio Canu Falcon 10x SuperNova Illumina Soap Denovo Discovar Platinus MaSuRCA Experimental design using Illumina Platform Estimate genome size:

More information

Sequence Assembly and Alignment. Jim Noonan Department of Genetics

Sequence Assembly and Alignment. Jim Noonan Department of Genetics Sequence Assembly and Alignment Jim Noonan Department of Genetics james.noonan@yale.edu www.yale.edu/noonanlab The assembly problem >>10 9 sequencing reads 36 bp - 1 kb 3 Gb Outline Basic concepts in genome

More information

Francisco García Quality Control for NGS Raw Data

Francisco García Quality Control for NGS Raw Data Contents Data formats Sequence capture Fasta and fastq formats Sequence quality encoding Quality Control Evaluation of sequence quality Quality control tools Identification of artifacts & filtering Practical

More information

Using New ThiNGS on Small Things. Shane Byrne

Using New ThiNGS on Small Things. Shane Byrne Using New ThiNGS on Small Things Shane Byrne Next Generation Sequencing New Things Small Things NGS Next Generation Sequencing = 2 nd generation of sequencing 454 GS FLX, SOLiD, GAIIx, HiSeq, MiSeq, Ion

More information

Bioinformatics small variants Data Analysis. Guidelines. genomescan.nl

Bioinformatics small variants Data Analysis. Guidelines. genomescan.nl Next Generation Sequencing Bioinformatics small variants Data Analysis Guidelines genomescan.nl GenomeScan s Guidelines for Small Variant Analysis on NGS Data Using our own proprietary data analysis pipelines

More information

SEQUENCE QUALITY CONSIDERATIONS FOR THE WET LAB

SEQUENCE QUALITY CONSIDERATIONS FOR THE WET LAB National Center for Emerging and Zoonotic Infectious Diseases SEQUENCE QUALITY CONSIDERATIONS FOR THE WET LAB Eija Trees, Ph.D., D.V.M. Chief, PulseNet Next Generation Subtyping Methods Unit PulseNet/OutbreakNet

More information

Welcome to the NGS webinar series

Welcome to the NGS webinar series Welcome to the NGS webinar series Webinar 1 NGS: Introduction to technology, and applications NGS Technology Webinar 2 Targeted NGS for Cancer Research NGS in cancer Webinar 3 NGS: Data analysis for genetic

More information

Tutorial for Stop codon reassignment in the wild

Tutorial for Stop codon reassignment in the wild Tutorial for Stop codon reassignment in the wild Learning Objectives This tutorial has two learning objectives: 1. Finding evidence of stop codon reassignment on DNA fragments. 2. Detecting and confirming

More information

Genome Assembly Background and Strategy

Genome Assembly Background and Strategy Genome Assembly Background and Strategy February 6th, 2017 BIOL 7210 - Faction I (Outbreak) - Genome Assembly Group Yanxi Chen Carl Dyson Zhiqiang Lin Sean Lucking Chris Monaco Shashwat Deepali Nagar Jessica

More information

DATA FORMATS AND QUALITY CONTROL

DATA FORMATS AND QUALITY CONTROL HTS Summer School 12-16th September 2016 DATA FORMATS AND QUALITY CONTROL Romina Petersen, University of Cambridge (rp520@medschl.cam.ac.uk) Luigi Grassi, University of Cambridge (lg490@medschl.cam.ac.uk)

More information

Functional annotation of metagenomes

Functional annotation of metagenomes Functional annotation of metagenomes Jeroen F. J. Laros Leiden Genome Technology Center Department of Human Genetics Center for Human and Clinical Genetics Introduction Functional analysis Objectives:

More information

Read Mapping and Variant Calling. Johannes Starlinger

Read Mapping and Variant Calling. Johannes Starlinger Read Mapping and Variant Calling Johannes Starlinger Application Scenario: Personalized Cancer Therapy Different mutations require different therapy Collins, Meredith A., and Marina Pasca di Magliano.

More information

Comparing a few SNP calling algorithms using low-coverage sequencing data

Comparing a few SNP calling algorithms using low-coverage sequencing data Yu and Sun BMC Bioinformatics 2013, 14:274 RESEARCH ARTICLE Open Access Comparing a few SNP calling algorithms using low-coverage sequencing data Xiaoqing Yu 1 and Shuying Sun 1,2* Abstract Background:

More information

Leonardo Mariño-Ramírez, PhD NCBI / NLM / NIH. BIOL 7210 A Computational Genomics 2/18/2015

Leonardo Mariño-Ramírez, PhD NCBI / NLM / NIH. BIOL 7210 A Computational Genomics 2/18/2015 Leonardo Mariño-Ramírez, PhD NCBI / NLM / NIH BIOL 7210 A Computational Genomics 2/18/2015 The $1,000 genome is here! http://www.illumina.com/systems/hiseq-x-sequencing-system.ilmn Bioinformatics bottleneck

More information

Matthew Tinning Australian Genome Research Facility. July 2012

Matthew Tinning Australian Genome Research Facility. July 2012 Next-Generation Sequencing: an overview of technologies and applications Matthew Tinning Australian Genome Research Facility July 2012 History of Sequencing Where have we been? 1869 Discovery of DNA 1909

More information

Computational assembly for prokaryotic sequencing projects

Computational assembly for prokaryotic sequencing projects Computational assembly for prokaryotic sequencing projects Lee Katz, Ph.D. Bioinformatician, Enteric Diseases Laboratory Branch January 21, 2015 Disclaimers The findings and conclusions in this presentation

More information

Whole-genome sequencing (WGS) of microbes employing nextgeneration sequencing (NGS) technologies enables pathogen

Whole-genome sequencing (WGS) of microbes employing nextgeneration sequencing (NGS) technologies enables pathogen Application Note Microbial whole-genome sequencing A novel, single-tube enzymatic fragmentation and library construction method enables fast turnaround times and improved data quality for microbial whole-genome

More information

THE RISE OF WHOLE GENOME SEQUENCING AS A SUBTYPING TOOL FOR MICROBIAL SOURCE TRACKING: FROM FUNDAMENTALS TO APPLICATIONS

THE RISE OF WHOLE GENOME SEQUENCING AS A SUBTYPING TOOL FOR MICROBIAL SOURCE TRACKING: FROM FUNDAMENTALS TO APPLICATIONS THE RISE OF WHOLE GENOME SEQUENCING AS A SUBTYPING TOOL FOR MICROBIAL SOURCE TRACKING: FROM FUNDAMENTALS TO APPLICATIONS STEAK EXPERT MEETING: ANGERS FRANCE JUNE, 2015 Kendra Nightingale, Ph.D. Inter national

More information

QIAseq Targeted Panel Analysis Plugin USER MANUAL

QIAseq Targeted Panel Analysis Plugin USER MANUAL QIAseq Targeted Panel Analysis Plugin USER MANUAL User manual for QIAseq Targeted Panel Analysis 1.1 Windows, macos and Linux June 18, 2018 This software is for research purposes only. QIAGEN Aarhus Silkeborgvej

More information