SMRT Analysis v2.2.0 Overview. 1. SMRT Analysis v SMRT Analysis v2.2.0 Overview. Notes:

Size: px
Start display at page:

Download "SMRT Analysis v2.2.0 Overview. 1. SMRT Analysis v2.2.0. 1.1 SMRT Analysis v2.2.0 Overview. Notes:"

Transcription

1 SMRT Analysis v2.2.0 Overview SMRT Analysis v SMRT Analysis v2.2.0 Overview Welcome to Pacific Biosciences' SMRT Analysis v2.2.0 Overview

2 1.2 Contents This module will introduce the new key features and benefits in SMRT Analysis v We will discuss SMRT Portal Enhancements and then describe upgrade requirements. Finally, we will show additional resources available for your reference.

3 1.3 Key Features & Benefits SMRT Analysis v2.2.0 Key Features and Benefits

4 1.4 New & Improved Application Analysis SMRT Analysis v2.2.0 software enables PacBio users to perform a wider range of scientific analyses for their research question. The software now has improved functionality for the study of transcriptomes, haplotypes and phasing with long amplicons, and minor variants in genomic samples. In addition, we have incorporated significant speed improvements to PacBio's Hierarchical Genome Assembly Process (HGAP). Finally, we have made workflow enhancements to SMRT Portal, our graphical user interface.

5 1.5 Feature Enhancements SMRT Analysis features a number of incremental advancements over previous releases. -For HGAP, notable improvements in include a 10x improvement in assembly time for microbial genomes, as well as inclusion of the diploid version of Quiver (consensus calling algorithm). - The Long-Amplicon Analysis module now includes support for filtering chimeric sequences. - The Minor-Variant algorithm has been updated to include a more sophisticated variant caller that can detect minor variants with as low as.5% frequency. - The transcriptome-analysis module (Iso-Seq application) now includes full-length transcript QC and clustering steps, in addition to mapping to a reference sequence.

6 1.6 Iso Seq Module SMRT Analysis v2.2.0 Iso-Seq Module

7 1.7 Iso Seq Method Full Length Transcripts The workflow for the Iso-Seq protocol is shown in this slide. Full-length cdna synthesis from poly(a) RNA using the Clontech SMARTer PCR cdna Synthesis Kit, followed by size selection and conversion to SMRTbell libraries is shown here. Full-length cdna libraries can be produced from as little as 1 ng of poly(a) RNA, or 2 ng total RNA. Following PacBio sequencing, the PacBio Iso-Seq software protocol in SMRT determines which transcripts are sequenced to full length. Analysis A full-length assignment is made on the basis of -detection of the 5' -end primer, 5' UTR, ORF, 3' UTR, polya tail, and 3' primer in a single read. Similar reads can be clustered together to generate a consensus non-redundant isoform transcript to be used for evidence-based gene models.

8 1.8 QC Visualization of Full Length Transcripts The Iso-Seq module provides QC metrics that might be of interest to the user such as the number of reads of insert, mean read length, quality, and number of passes. The classify output feature displays a histogram of the distribution of read length as well as a breakdown of full-length reads, non-full-length reads, and filtered short reads. Also available is a cluster output that provides a summary of the length distribution of the non-redundant consensus sequence for isoform reads.

9 1.9 Long Amplicon Analysis SMRT Analysis v2.2.0 Long-Amplicon Analysis

10 1.10 Process for Long Amplicon Analysis Long-amplicon analysis has been updated with the implementation of chimera filtering. The workflow involves the following steps: 1. De-multiplexing of reads by Barcode 2. Finding overlaps between reads. Reads belonging to the same gene will cluster together. 3. Fine tuning those clusters at a SNP level 4. Recursively partitioning to determine different phases 5. Applying Quiver to determine haplotypes 6. Post-processing filters such as chimera filtering

11 1.11 Minor Variant Analysis SMRT Analysis Minor-Variant Analysis

12 1.12 Detection of Minor Variants The minor variant module calls minor variants in a heterogeneous dataset that is mapped against a user-provided reference sequence. A major feature of the current version of the algorithm is that it learns an error model for the user's data. The algorithm works by aligning Reads of Insert sequences to the reference sequence. It then exhaustively scores alignments of query sequences to the reference using a fixed window. The output format consists of variant calls in vcf and csv formats. The algorithm is tuned for sensitivity: >99% sensitivity >98% specificity The algorithm can detect down to 0.5% abundance, data permitting.

13 1.13 Minor Variant Protocol Shown here is an example output from the Minor Variant protocol. The protocol is launched through SMRT Portal. A set of diagnostic plots is shown, and a VCF file with the frequency of each detected mutation is able to be exported from the "Analysis" sub-tab. Subsequent release versions will have support for phasing analysis.

14 1.14 HGAP SMRT Analysis v2.2.0 HGAP

15 1.15 Updated HGAP HGAP 2 is transitioned out of beta and contains bug fixes and algorithm improvements to HGAP 1 Microbial genome assembly now runs <1day. HGAP 3 (beta) is optimized for speed with up to 10-times shorter wall-clock time for microbial genomes. Command line HGAP using smrtpipe.py supports assembly of larger genomes.

16 1.16 HGAP: Marked Speed Improvements While Maintaining Comparable Assembly Quality As illustrated in the graph above, HGAP 3 shows significant improvement in speed compared to previous releases. The correction phase of the software was significantly improved from HGAP 1. The beta version, HGAP 3, incorporates further improvements in the draft phase to drive down assembly time.

17 1.17 Summary of Protocol Changes Shown here is a summary of protocol changes in SMRT Analysis v For the pre-assembly step, the pbdagcon algorithm drives much of the speed improvements in HGAP. Nomenclature changes regarding the Reads of Insert protocol now reflect a more sophisticated error model (Quiver) that works on sub-reads for consensus calling. Bar coding functionality has been added to the RS filter module, and Bridgemapper has been transitioned out of beta status.

18 1.18 SMRT Portal Improvements SMRT Analysis SMRT Portal Improvements

19 1.19 Dialog Boxes We have added a new functionality to SMRT Portal that groups protocols by application area, thereby simplifying navigation. The user is presented with this dialog on the Design-Job page. The user has an option to opt out and not view this dialog box during future logins.

20 1.20 N50 Metric We are also implementing the N50 metric, which is a more informative measure of readlength distribution. N50 read length is the value at which 50% of the bases are derived from read lengths greater than or equal to this value.

21 1.21 Updated Quiver A new Quiver consensus-calling training is implemented in SMRT Analysis v With this improved training, consensus accuracy with P5-C3 improves by 5%. However, this new training does not affect P4-C2 chemistry. This new training was tested on three 20 kb libraries (E. coli, S. aureus, and R. palustris).

22 1.22 Upgrade Requirements SMRT Analysis v2.2.0 Software Availability and Upgrade Requirements

23 1.23 Software Availability SMRT Analysis v2.2.0 will be available from pacbiodevnet.com This is an upgrade of secondary-analysis software only. The user will not experience instrument downtime during the upgrade. Install documentation and release notes are available, as well as FAQs.

24 1.24 Upgrade Requirements Upgrade is supported from SMRT Analysis v2.1.1 only. User cannot skip level upgrades. Upgrade Requirements Supported Operating Systems: Ubuntu 12.04, 10.04, 8.04 CentOS 6.3, 5.6, 5.3 Bash, Linux Standard Base (LSB) No MySQL, Perl dependencies SMRT Analysis v2.2.0 is backwards compatible with previous versions. Links to documentation on PacBio DevNet pacbiodevnet.com Bundled MySQL server No external MySQL needed Single OS installation tarball

25 Patch tarball concept introduced Very small self-extracting tarball which can be used to workaround bugs found in the field (beta or production) Replaces manual fixes and edits by the customer Can run it as part of the installer or upgrader command line (i.e. can patch the installer/updater itself) Can also run after install/upgrade completed (to fix an existing install) Similar to patch tarball used for SMRT Analysis v Additional Resources Additional Resources

26 1.26 Resources Here are some additional resources, grouped by topic area.

27 1.27 Resources Some more resources for your interest.

28 1.28 Thank You Thank you for your participation. For more information, please contact your local PacBio Field Applications Scientist or PacBio Account Representative.

Software Getting Started Guide

Software Getting Started Guide Software Getting Started Guide For Research Use Only. Not for use in diagnostic procedures. P/N 001-097-569-03 Copyright 2010-2013, Pacific Biosciences of California, Inc. All rights reserved. Information

More information

Using Illumina BaseSpace Apps to Analyze RNA Sequencing Data

Using 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 information

Next Generation Sequencing

Next 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 information

New Technologies for Sensitive, Low-Input RNA-Seq. Clontech Laboratories, Inc.

New 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 information

How to Run the PacBio RS II Instrument. 1. Run Instrument. 1.1 How to Run the RS II Instrument

How to Run the PacBio RS II Instrument. 1. Run Instrument. 1.1 How to Run the RS II Instrument How to Run the PacBio RS II Instrument 100 338 600 01 1. Run Instrument 1.1 How to Run the RS II Instrument Welcome to Pacific Biosciences' How to Run the PacBio RS II Instrument training module. This

More information

TCB No. 2012-008 September 2012. Technical Bulletin. GS FLX+ System & GS FLX System. Installation of 454 Sequencing System Software v2.

TCB No. 2012-008 September 2012. Technical Bulletin. GS FLX+ System & GS FLX System. Installation of 454 Sequencing System Software v2. TCB No. 2012-008 September 2012 Technical Bulletin GS FLX+ System & GS FLX System Installation of 454 Sequencing System Software v2.8 Summary This document describes how to upgrade the 454 Sequencing System

More information

Welcome to Pacific Biosciences' Introduction to SMRTbell Template Preparation.

Welcome to Pacific Biosciences' Introduction to SMRTbell Template Preparation. Introduction to SMRTbell Template Preparation 100 338 500 01 1. SMRTbell Template Preparation 1.1 Introduction to SMRTbell Template Preparation Welcome to Pacific Biosciences' Introduction to SMRTbell

More information

Introduction to NGS data analysis

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 information

SMRT Analysis Software Installation (v2.3.0)

SMRT Analysis Software Installation (v2.3.0) SMRT Analysis Software Installation (v2.3.0) Introduction This document describes the basic requirements for installing SMRT Analysis v2.3.0 on a customer system. SMRT Analysis is designed to be installed

More information

Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS)

Introduction 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 information

Vector NTI Advance 11 Quick Start Guide

Vector NTI Advance 11 Quick Start Guide Vector NTI Advance 11 Quick Start Guide Catalog no. 12605050, 12605099, 12605103 Version 11.0 December 15, 2008 12605022 Published by: Invitrogen Corporation 5791 Van Allen Way Carlsbad, CA 92008 U.S.A.

More information

PreciseTM Whitepaper

PreciseTM 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 information

Statistics Output Guide

Statistics Output Guide Statistics Output Guide Introduction This document describes the file stats.xml, which is produced by the primary analysis pipeline. This file packages summary statistics from a single movie acquisition.

More information

SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications

SeqScape 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 information

AGILENT S BIOINFORMATICS ANALYSIS SOFTWARE

AGILENT S BIOINFORMATICS ANALYSIS SOFTWARE ACCELERATING PROGRESS IS IN OUR GENES AGILENT S BIOINFORMATICS ANALYSIS SOFTWARE GENESPRING GENE EXPRESSION (GX) MASS PROFILER PROFESSIONAL (MPP) PATHWAY ARCHITECT (PA) See Deeper. Reach Further. BIOINFORMATICS

More information

Ion Torrent Amplicon Sequencing

Ion Torrent Amplicon Sequencing APPLICATION NOTE Amplicon Sequencing Ion Torrent Amplicon Sequencing Introduction The ability to sequence a genome or a portion of a genome has enabled researchers to begin to understand how the genetic

More information

LifeScope Genomic Analysis Software 2.5

LifeScope 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 information

Delivering the power of the world s most successful genomics platform

Delivering 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 information

454 Sequencing System Software Manual, v 2.5p1

454 Sequencing System Software Manual, v 2.5p1 , v 2.5p1 August 2010 For life science research only. Not for use in diagnostic procedures. 454 Sequencing System Software Manual Software v. 2.5p1, August 2010 Table of Contents Preface...4 About this

More information

Needle shearing DNA for PacBio >20 kb libraries.

Needle shearing DNA for PacBio >20 kb libraries. Needle shearing DNA for PacBio >20 kb libraries. NOV2013, Paul Coupland, Liz Sheridan Wellcome Trust Sanger Institute pc10@sanger.ac.uk This protocol outlines a shearing technique we use for preparing

More information

MiSeq: Imaging and Base Calling

MiSeq: 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 information

Focusing 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 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 information

NaviCell Data Visualization Python API

NaviCell Data Visualization Python API NaviCell Data Visualization Python API Tutorial - Version 1.0 The NaviCell Data Visualization Python API is a Python module that let computational biologists write programs to interact with the molecular

More information

Description: Molecular Biology Services and DNA Sequencing

Description: 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 information

AS4.1 190509 Replaces 260806 Page 1 of 50 ATF. Software for. DNA Sequencing. Operators Manual. Assign-ATF is intended for Research Use Only (RUO):

AS4.1 190509 Replaces 260806 Page 1 of 50 ATF. Software for. DNA Sequencing. Operators Manual. Assign-ATF is intended for Research Use Only (RUO): Replaces 260806 Page 1 of 50 ATF Software for DNA Sequencing Operators Manual Replaces 260806 Page 2 of 50 1 About ATF...5 1.1 Compatibility...5 1.1.1 Computer Operator Systems...5 1.1.2 DNA Sequencing

More information

All in a highly interactive, easy to use Windows environment.

All 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 information

SNPbrowser Software v3.5

SNPbrowser Software v3.5 Product Bulletin SNP Genotyping SNPbrowser Software v3.5 A Free Software Tool for the Knowledge-Driven Selection of SNP Genotyping Assays Easily visualize SNPs integrated with a physical map, linkage disequilibrium

More information

SMRT Analysis Software Installation (v1.4.0)

SMRT Analysis Software Installation (v1.4.0) SMRT Analysis Software Installation (v1.4.0) Introduction This document describes the basic requirements for installing SMRT Analysis v1.4.0 on a customer system. This document is for use by Field Service

More information

DATA MINING TOOL FOR INTEGRATED COMPLAINT MANAGEMENT SYSTEM WEKA 3.6.7

DATA MINING TOOL FOR INTEGRATED COMPLAINT MANAGEMENT SYSTEM WEKA 3.6.7 DATA MINING TOOL FOR INTEGRATED COMPLAINT MANAGEMENT SYSTEM WEKA 3.6.7 UNDER THE GUIDANCE Dr. N.P. DHAVALE, DGM, INFINET Department SUBMITTED TO INSTITUTE FOR DEVELOPMENT AND RESEARCH IN BANKING TECHNOLOGY

More information

BarTender Web Print Server

BarTender Web Print Server The World's Leading Software for Label, Barcode, RFID & Card Printing White Paper BarTender Web Print Server Web-based Software for Printing Barcodes, Labels, ID Cards and more. Contents Introduction to

More information

NGS data analysis. Bernardo J. Clavijo

NGS 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 information

Single-Cell DNA Sequencing with the C 1. Single-Cell Auto Prep System. Reveal hidden populations and genetic diversity within complex samples

Single-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 information

GenomeStudio Data Analysis Software

GenomeStudio Data Analysis Software GenomeStudio Analysis Software Illumina has created a comprehensive suite of data analysis tools to support a wide range of genetic analysis assays. This single software package provides data visualization

More information

GenomeStudio Data Analysis Software

GenomeStudio Data Analysis Software GenomeStudio Data Analysis Software Illumina has created a comprehensive suite of data analysis tools to support a wide range of genetic analysis assays. This single software package provides data visualization

More information

Core Facility Genomics

Core 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 information

On-line supplement to manuscript Galaxy for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

On-line supplement to manuscript Galaxy for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly On-line supplement to manuscript Galaxy for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly DANIEL BLANKENBERG, JAMES TAYLOR, IAN SCHENCK, JIANBIN HE, YI ZHANG, MATTHEW

More information

GeneChip Sequence Analysis Software (GSEQ) is used to analyze data from the Resequencing Arrays

GeneChip Sequence Analysis Software (GSEQ) is used to analyze data from the Resequencing Arrays GeneChip Sequence Analysis Software 4.1 Note For more information, Please refer to the Affymetrix GeneChip Sequence Analysis Software User s Guide Version 4.1 guidebook & Quick Reference Card I. GSEQ Introduction

More information

Public Health Laboratory Workforce Development Bioinformatics

Public Health Laboratory Workforce Development Bioinformatics Public Health Laboratory Workforce Development Bioinformatics Templates for Course Development Contents Overview... 1 Going Beyond the Introductory Courses... 1 Course Templates... 3 Template 1: Introduction

More information

Sequencing power for every scale. Systems for every application, for every lab.

Sequencing power for every scale. Systems for every application, for every lab. Sequencing power for every scale. Systems for every application, for every lab. Proven sequencing technology. Accelerate your research. Achieve your next breakthrough. What started as novel Illumina chemistry,

More information

ONE WORKFLOW. ONE PARTNER. ACTIONABLE INSIGHTS. Sample to Insight

ONE WORKFLOW. ONE PARTNER. ACTIONABLE INSIGHTS. Sample to Insight ONE WORKFLOW. ONE PARTNER. ACTIONABLE INSIGHTS. Sample to Insight (NGS) Nucleic Acid More actionable data and insights in one go. More confidence at one glance. A small step for you, a giant leap for your

More information

Advanced analytics at your hands

Advanced analytics at your hands 2.3 Advanced analytics at your hands Neural Designer is the most powerful predictive analytics software. It uses innovative neural networks techniques to provide data scientists with results in a way previously

More information

UGENE Quick Start Guide

UGENE 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 information

Lecture 11 Data storage and LIMS solutions. Stéphane LE CROM lecrom@biologie.ens.fr

Lecture 11 Data storage and LIMS solutions. Stéphane LE CROM lecrom@biologie.ens.fr Lecture 11 Data storage and LIMS solutions Stéphane LE CROM lecrom@biologie.ens.fr Various steps of a DNA microarray experiment Experimental steps Data analysis Experimental design set up Chips on catalog

More information

Data Analysis for Ion Torrent Sequencing

Data 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 information

Go 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. 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 information

Computational Requirements

Computational Requirements Workshop on Establishing a Central Resource of Data from Genome Sequencing Projects Computational Requirements Steve Sherry, Lisa Brooks, Paul Flicek, Anton Nekrutenko, Kenna Shaw, Heidi Sofia High-density

More information

Chapter 2. imapper: A web server for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes

Chapter 2. imapper: A web server for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes Chapter 2. imapper: A web server for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes 2.1 Introduction Large-scale insertional mutagenesis screening in

More information

FINACS Version 3. Administrator s Plus Accounting. An Overview of New Features

FINACS Version 3. Administrator s Plus Accounting. An Overview of New Features FINACS Version 3 Administrator s Plus Accounting An Overview of New Features Table of Contents Interface... 2 Portfolio... 4 Billing and Transactions... 5 Billing Services... 5 Transaction Details... 6

More information

454 Sequencing System Software Manual Version 2.6

454 Sequencing System Software Manual Version 2.6 454 Sequencing System Software Manual Version 2.6 Part C: May 2011 Instrument / Kit GS Junior / Junior GS FL+ / L+ GS FL+ / LR70 GS FL / LR70 For life science research only. Not for use in diagnostic procedures.

More information

Welcome to the Plant Breeding and Genomics Webinar Series

Welcome to the Plant Breeding and Genomics Webinar Series Welcome to the Plant Breeding and Genomics Webinar Series Today s Presenter: Dr. Candice Hansey Presentation: http://www.extension.org/pages/ 60428 Host: Heather Merk Technical Production: John McQueen

More information

Pandora Administrator Training (PAT-2010)

Pandora Administrator Training (PAT-2010) Pandora Administrator Training (PAT-2010) 1. Introduction to Pandora FMS. History and evolution of Pandora FMS. Main features of Pandora FMS. 2. Pandora FMS Architecture. Overview Software agents Servers

More information

TruSeq Custom Amplicon v1.5

TruSeq 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 information

Release Notes scvenus 2.3.0

Release Notes scvenus 2.3.0 June 2008 IT Services Release Notes scvenus 2.3.0 Operational Concepts Security Solutions Technical Release Notes What's New? Supported / New Operating Systems Sales Email Support / Mailing Lists Web Portal

More information

Idera SQL Diagnostic Manager Management Pack Guide for System Center Operations Manager. Install Guide. Idera Inc., Published: April 2013

Idera SQL Diagnostic Manager Management Pack Guide for System Center Operations Manager. Install Guide. Idera Inc., Published: April 2013 Idera SQL Diagnostic Manager Management Pack Guide for System Center Operations Manager Install Guide Idera Inc., Published: April 2013 Contents Introduction to the Idera SQL Diagnostic Manager Management

More information

Geospiza s Finch-Server: A Complete Data Management System for DNA Sequencing

Geospiza s Finch-Server: A Complete Data Management System for DNA Sequencing KOO10 5/31/04 12:17 PM Page 131 10 Geospiza s Finch-Server: A Complete Data Management System for DNA Sequencing Sandra Porter, Joe Slagel, and Todd Smith Geospiza, Inc., Seattle, WA Introduction The increased

More information

Partek Flow Installation Guide

Partek Flow Installation Guide Partek Flow Installation Guide Partek Flow is a web based application for genomic data analysis and visualization, which can be installed on a desktop computer, compute cluster or cloud. Users can access

More information

Genome Informatics Course: UCSC Genome Browser

Genome Informatics Course: UCSC Genome Browser Genome Informatics Course: UCSC Genome Browser Shamith Samarajiwa Statistics and Computational Biology group (Tavaré lab) 5th Dec 2014, CRUK Cambridge Institute Introduction main sections: 1. UCSC Genome

More information

Review Manager Guide

Review Manager Guide Review Manager Guide v8.0 May 10, 2013 For the most recent version of this document, visit kcura's Documentation Site. Table of Contents 1 Review Manager overview 4 1.1 Review Manager life cycle 4 1.2

More information

SEQUENCING. From Sample to Sequence-Ready

SEQUENCING. 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 information

W3Perl A free logfile analyzer

W3Perl A free logfile analyzer W3Perl A free logfile analyzer Features Works on Unix / Windows / Mac View last entries based on Perl scripts Web / FTP / Squid / Email servers Session tracking Others log format can be added easily Detailed

More information

Analysis of ChIP-seq data in Galaxy

Analysis 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 information

FileMaker Pro and Microsoft Office Integration

FileMaker Pro and Microsoft Office Integration FileMaker Pro and Microsoft Office Integration page Table of Contents Executive Summary...3 Introduction...3 Top Reasons to Read This Guide...3 Before You Get Started...4 Downloading the FileMaker Trial

More information

GenomeSpace Architecture

GenomeSpace Architecture GenomeSpace Architecture The primary services, or components, are shown in Figure 1, the high level GenomeSpace architecture. These include (1) an Authorization and Authentication service, (2) an analysis

More information

University of Glasgow - Programme Structure Summary C1G5-5100 MSc Bioinformatics, Polyomics and Systems Biology

University of Glasgow - Programme Structure Summary C1G5-5100 MSc Bioinformatics, Polyomics and Systems Biology University of Glasgow - Programme Structure Summary C1G5-5100 MSc Bioinformatics, Polyomics and Systems Biology Programme Structure - the MSc outcome will require 180 credits total (full-time only) - 60

More information

Real-time quantitative RT -PCR (Taqman)

Real-time quantitative RT -PCR (Taqman) Real-time quantitative RT -PCR (Taqman) Author: SC, Patti Lab, 3/03 This is performed as a 2-step reaction: 1. cdna synthesis from DNase 1-treated total RNA 2. PCR 1. cdna synthesis (Advantage RT-for-PCR

More information

CLC Sequence Viewer USER MANUAL

CLC Sequence Viewer USER MANUAL CLC Sequence Viewer USER MANUAL Manual for CLC Sequence Viewer 7.6.1 Windows, Mac OS X and Linux September 3, 2015 This software is for research purposes only. QIAGEN Aarhus A/S Silkeborgvej 2 Prismet

More information

imc FAMOS 6.3 visualization signal analysis data processing test reporting Comprehensive data analysis and documentation imc productive testing

imc FAMOS 6.3 visualization signal analysis data processing test reporting Comprehensive data analysis and documentation imc productive testing imc FAMOS 6.3 visualization signal analysis data processing test reporting Comprehensive data analysis and documentation imc productive testing imc FAMOS ensures fast results Comprehensive data processing

More information

Implementation Overview. Digital Rights Management (DRM) Solution

Implementation Overview. Digital Rights Management (DRM) Solution Implementation Overview Digital Rights Management (DRM) Solution DRM Introduction E-Book Sytems Digital Rights Management solution allows for a secure distribution of FlipBooks to their readers. DRM can

More information

Visualization with the Integrative Genomics Viewer (IGV)

Visualization with the Integrative Genomics Viewer (IGV) Ecole de Bioinformatique Aviesan - Integrative Genomics Viewer (IGV) 1 Visualization with the Integrative Genomics Viewer (IGV) Elodie Girard Institut Curie U900 Inserm Mines ParisTech Ecole de Bioinformatique

More information

Frequently Asked Questions Next Generation Sequencing

Frequently Asked Questions Next Generation Sequencing Frequently Asked Questions Next Generation Sequencing Import These Frequently Asked Questions for Next Generation Sequencing are some of the more common questions our customers ask. Questions are divided

More information

NECC History. Karl V. Steiner 2011 Annual NECC Meeting, Orono, Maine March 15, 2011

NECC History. Karl V. Steiner 2011 Annual NECC Meeting, Orono, Maine March 15, 2011 NECC History Karl V. Steiner 2011 Annual NECC Meeting, Orono, Maine March 15, 2011 EPSCoR Cyberinfrastructure Workshop First regional NENI (now NECC) Workshop held in Vermont in August 2007 Workshop heldinkentucky

More information

BioHPC Web Computing Resources at CBSU

BioHPC 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 information

The Galaxy workflow. George Magklaras PhD RHCE

The Galaxy workflow. George Magklaras PhD RHCE The Galaxy workflow George Magklaras PhD RHCE Biotechnology Center of Oslo & The Norwegian Center of Molecular Medicine University of Oslo, Norway http://www.biotek.uio.no http://www.ncmm.uio.no http://www.no.embnet.org

More information

Decomposition into Parts. Software Engineering, Lecture 4. Data and Function Cohesion. Allocation of Functions and Data. Component Interfaces

Decomposition into Parts. Software Engineering, Lecture 4. Data and Function Cohesion. Allocation of Functions and Data. Component Interfaces Software Engineering, Lecture 4 Decomposition into suitable parts Cross cutting concerns Design patterns I will also give an example scenario that you are supposed to analyse and make synthesis from The

More information

/ Administrator Training PAT-2012

/ Administrator Training PAT-2012 / Administrator Training PAT-2012 TRAINING REQUIREMENTS Duration: 15 hours Average networking knowledge Average Linux knowledge 1 computer per student Network in the classroom to connect all hosts (including

More information

EINTE LAB EXERCISES LAB EXERCISE #5 - SIP PROTOCOL

EINTE LAB EXERCISES LAB EXERCISE #5 - SIP PROTOCOL EINTE LAB EXERCISES LAB EXERCISE #5 - SIP PROTOCOL PREPARATIONS STUDYING SIP PROTOCOL The aim of this exercise is to study the basic aspects of the SIP protocol. Before executing the exercise you should

More information

WebFOCUS RStat. RStat. Predict the Future and Make Effective Decisions Today. WebFOCUS RStat

WebFOCUS RStat. RStat. Predict the Future and Make Effective Decisions Today. WebFOCUS RStat Information Builders enables agile information solutions with business intelligence (BI) and integration technologies. WebFOCUS the most widely utilized business intelligence platform connects to any enterprise

More information

BarTender s.net SDKs

BarTender s.net SDKs The World's Leading Software for Label, Barcode, RFID & Card Printing White Paper BarTender s.net SDKs Programmatically Controlling BarTender using C# and VB.NET Contents Overview of BarTender.NET SDKs...

More information

Molecular typing of VTEC: from PFGE to NGS-based phylogeny

Molecular typing of VTEC: from PFGE to NGS-based phylogeny Molecular typing of VTEC: from PFGE to NGS-based phylogeny Valeria Michelacci 10th Annual Workshop of the National Reference Laboratories for E. coli in the EU Rome, November 5 th 2015 Molecular typing

More information

Welcome to the IBM Education Assistant module for Tivoli Storage Manager version 6.2 Hyper-V backups. hyper_v_backups.ppt.

Welcome to the IBM Education Assistant module for Tivoli Storage Manager version 6.2 Hyper-V backups. hyper_v_backups.ppt. Welcome to the IBM Education Assistant module for Tivoli Storage Manager version 6.2 Hyper-V backups. Page 1 of 21 You are familiar with Tivoli Storage Manager version 5.5 or higher. Page 2 of 21 When

More information

CA Performance Center

CA Performance Center CA Performance Center Release Notes Release 2.3.3 This Documentation, which includes embedded help systems and electronically distributed materials, (hereinafter referred to as the Documentation ) is for

More information

Ovation Operator Workstation for Microsoft Windows Operating System Data Sheet

Ovation Operator Workstation for Microsoft Windows Operating System Data Sheet Ovation Operator Workstation for Microsoft Windows Operating System Features Delivers full multi-tasking operation Accesses up to 200,000 dynamic points Secure standard operating desktop environment Intuitive

More information

Next generation DNA sequencing technologies. theory & prac-ce

Next 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 information

Figure 2: System Flow Diagram for Workflow Management

Figure 2: System Flow Diagram for Workflow Management 5. WORKFLOW MANAGEMENT The developed system EASKB uses the open source content management system called Drupal ([2]). A Content Management System - CMS is a tool that enables many user friendly features

More information

HP Application Lifecycle Management (ALM)

HP Application Lifecycle Management (ALM) HP Application Lifecycle Management (ALM) Knowledge Share Maheshwar Salendra Date : 12/02/2012 AGENDA: Introduction to ALM ALM Functionality by Edition ALM Home page Side bars: Management Requirements

More information

Standards, Guidelines and Best Practices for RNA-Seq V1.0 (June 2011) The ENCODE Consortium

Standards, Guidelines and Best Practices for RNA-Seq V1.0 (June 2011) The ENCODE Consortium Standards, Guidelines and Best Practices for RNA-Seq V1.0 (June 2011) The ENCODE Consortium I. Introduction: Sequence based assays of transcriptomes (RNA-seq) are in wide use because of their favorable

More information

Amplicon Template Preparation and Sequencing

Amplicon Template Preparation and Sequencing Please note: the shared protocols described herein may not have been validated by Pacific Biosciences and are provided as-is and without any warranty. Use of these protocols is offered to those customers

More information

Gene Expression Assays

Gene Expression Assays APPLICATION NOTE TaqMan Gene Expression Assays A mpl i fic ationef ficienc yof TaqMan Gene Expression Assays Assays tested extensively for qpcr efficiency Key factors that affect efficiency Efficiency

More information

NAIP Consortium Strengthening Statistical Computing for NARS www.iasri.res.in/sscnars SAS Enterprise Business Intelligence

NAIP Consortium Strengthening Statistical Computing for NARS www.iasri.res.in/sscnars SAS Enterprise Business Intelligence NAIP Consortium Strengthening Statistical Computing for NARS www.iasri.res.in/sscnars SAS Enterprise Business Intelligence BY Rajender Parsad, Neeraj Monga, Satyajit Dwivedi, RS Tomar, RK Saini Contents

More information

NNMi120 Network Node Manager i Software 9.x Essentials

NNMi120 Network Node Manager i Software 9.x Essentials NNMi120 Network Node Manager i Software 9.x Essentials Instructor-Led Training For versions 9.0 9.2 OVERVIEW This course is designed for those Network and/or System administrators tasked with the installation,

More information

MultiExperiment Viewer Quickstart Guide

MultiExperiment Viewer Quickstart Guide MultiExperiment Viewer Quickstart Guide Table of Contents: I. Preface - 2 II. Installing MeV - 2 III. Opening a Data Set - 2 IV. Filtering - 6 V. Clustering a. HCL - 8 b. K-means - 11 VI. Modules a. T-test

More information

DeCyder Extended Data Analysis module Version 1.0

DeCyder Extended Data Analysis module Version 1.0 GE Healthcare DeCyder Extended Data Analysis module Version 1.0 Module for DeCyder 2D version 6.5 User Manual Contents 1 Introduction 1.1 Introduction... 7 1.2 The DeCyder EDA User Manual... 9 1.3 Getting

More information

WhatsVirtual for WhatsUp Gold v16.0 User Guide

WhatsVirtual for WhatsUp Gold v16.0 User Guide WhatsVirtual for WhatsUp Gold v16.0 User Guide Contents Welcome Welcome to WhatsVirtual... 1 Using WhatsVirtual Discovering virtual devices... 2 Viewing discovery output... 4 Manage and monitor virtual

More information

Review Manager Guide

Review Manager Guide Review Manager Guide January 26, 2016 - Version 8.2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

More information

Bioinformatics Grid - Enabled Tools For Biologists.

Bioinformatics Grid - Enabled Tools For Biologists. Bioinformatics Grid - Enabled Tools For Biologists. What is Grid-Enabled Tools (GET)? As number of data from the genomics and proteomics experiment increases. Problems arise for the current sequence analysis

More information

SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis

SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis Goal: This tutorial introduces several websites and tools useful for determining linkage disequilibrium

More information

The 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 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 information

How Sequencing Experiments Fail

How 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 information

Visualization methods for patent data

Visualization methods for patent data Visualization methods for patent data Treparel 2013 Dr. Anton Heijs (CTO & Founder) Delft, The Netherlands Introduction Treparel can provide advanced visualizations for patent data. This document describes

More information

Nick Sophinos CEO WDean Medical

Nick Sophinos CEO WDean Medical WDean Medical Patient and Family Portal Patient Portal Communication is essential Nick Sophinos CEO WDean Medical! WDean Medical Empowering Care Overview WDean Medical's Patient and Family Portal module

More information