For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.

FINAL

Spec SheetLifeScope™ Genomic Analysis Solutions

LifeScope™ Genomic Analysis SolutionsOptimal analysis for 5500 Series Genetic Analyzers

OverviewLeveraging years of customer feedback and development of analysis tools for 5500 Series data, new LifeScope™ Genomic Analysis Solutions enable faster translation of next-generation sequencing (NGS) data to biologically meaningful results for every biologist and life scientist. Designed to match the revolutionary accuracy of the next-generation 5500 Series Genetic Analyzers with Exact Call Chemistry (ECC), LifeScope™ streamlines your research with its ease of use, expediting your experi-ment from sample to results.

Data analysis you can trustLifeScope™ Genomic Analysis Solutions build on the accuracy of the 5500 Series Genetic Analyzers with

ECC, bringing you system-optimized algorithms to generate high-quality data. You can work directly in base space with LifeScope™ Genomic Analysis Solutions to analyze your data effortlessly.

Choose what works for youLifeScope™ Genomic Analysis Solutions offer a variety of options to enable you to meet your research requirements. Whether you are running large-scale genomic experiments or small- to medium-sized projects, you can install LifeScope™ Server Software on your own hardware, or select a LifeScope™ Workstation, Cluster, or Cloud com-puting option to move your research

Key benefits•Maximumproductivityand

efficiency—developed to seamlessly integrate with 5500 Series Genetic Analyzers

•Highlyaccurateanalysis—performance-tuned algorithms for the 5500 Series and Exact Call Chemistry (ECC) Module helps give high-quality results

•Matchyourresearchneeds—flexible solutions including hardware and software options to fit your requirements

•Straightforwardanalysis—push-button workflows, intuitive user interface, and secure project management are easy to use

•Fasterruntimes—optimized mapping and smaller file formats give rapid results

•Streamlineyourresearch—annotations, reports, and visualization tools simplify data interpretation

Figure1.PredefinedanalysisworkflowsinLifeScope™ServerSoftware.

Figure2.VisualizationofdatainLifeScope™ServerSoftware.

forward within your budget.

Analysis made easyBiologists will find 5500 Series data analysis easier than ever with the intuitive, sleek graphical user inter-face of LifeScope™ Server Software. Within the predefined workflows for a wide range of applications, you can choose the preset defaults optimized

for your application, or modify to your expert settings.

Get you there faster Discovering relevant biological data is even closer at hand with LifeScope™ Genomic Analysis Solutions. Results views with summarized data reports provide the data you need, bringing you one step closer to publication. Seamless connectivity to visualization tools like the Broad Institute Integrative Genomics Viewer (IGV) and Circos plots let you explore your data set and visualize genomic alterations with publication-quality images and well-established tools.

Table1.SpecificationsforLifeScope™ServerSoftware.

LifeScope™ Server Software specifications1

Systemcomponents Complete server- and client-side software for sequence mapping and variant detection

Capacity Designed to analyze billions of reads from the 5500 Series Genetic Analyzers

Mappingtime 10 hr for 1 billion 50 bp resequencing fragment data on 4-node cluster

Datainput • Full support for .xsq file format• Ability to process base space (when using the Exact Call Chemistry Module) and color space

sequence outputs

Dataoutput • BAM file of mapped reads• Annotated variant reports• Numerous charting and reporting formats, including Circos output• Seamless interoperability with the Broad Institute Integrative Genomics Viewer*• Interoperability with Partek® statistical and visualization tools*

Supportedworkflows • Whole genome sequencing• Targeted resequencing• Low-frequency variant detection• Whole exome sequencing• Whole transcriptome RNA sequencing• Small RNA sequencing• SNP detection• Large and small indel detection• Copy number variation detection• Inversion detection• Exon counting• Junction finding• Fusion transcript detection

Workflowconfiguration • Graphically driven configuration of multistep analysis workflows• Ability to save and reuse workflows

Projectmanagement • Secure project-based data management specific to each user• Projects can be stored and data reanalyzed

Licenseoptions • Annual Named User or Concurrent User licenses (5 licenses included in Core Server Software pack)

• Supplemental User licenses available for groups requiring more than 5 Named or Concurrent User licenses

Technicalsupport Technical support included in the license fee for the term of the license

Softwareupdates Patches and updates included in the license fee for the term of the license

Minimumclusterhardwareandsoftwarerequirements

• 4-node, 32-core, 2 GHz cluster configuration• Head node: dual core, 100 Gb scratch and 8 GB or more memory• 24 GB RAM per node• Compute cache per node: 500 GB• Local storage: 12 TB total storage (RAID 5 recommended, providing ~9.5 TB usable storage)• Supported operating systems: 64-bit CentOS 4.7 to 5.7, or RedHat 4.7 to 5.7• IB, or 1GigE or higher• Job scheduler software: PBS Torque 2.3 or higher, SGE 6.2 or higher, LSF 7.6 or higher

Graphicalinterfacerequirements • Windows XP SP3 , CentOS 4.x, or Mac OS® X v10.5• Internet Explorer® 6 or Firefox 3.6• JRE 1.6• 2 GB RAM• 1024 x 768 display monitor or higher

1Specifications subject to change.*Requires separate licenses for Broad Institute IGV and partek® Software, available from their respective vendors.

For research use only. Not intended for any animal or human therapeutic or diagnostic use. ©2012 Life Technologies Corporation. All rights reserved. The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners.CO016830112

Table2.SpecificationsforLifeScope™WorkstationandCluster.*

Hardware specifications1 Workstation Cluster

Systemcomponents Turnkey, desk-side workstation with preinstalled LifeScope™ Server Software, performance-tested and verified prior to shipping

High-performance, expandable compute cluster with preinstalled LifeScope™ Server Software, performance-tested and verified prior to shipping

Dimensions(W×D×H) 175 mm x 755 mm x 460 mm 595 mm x 1,090 mm x 1,190 mm

Mappingtime 10 hr for 600 million 50 bp (fragment) 6 hr for 600 million 50 bp (fragment) on 4-node cluster

LifeScope™ServerSoftwarelicenseoptions2

• Annual Named User or Concurrent User licenses (5 licenses included in Core Server Software pack)• Supplemental User licenses available for groups requiring more than 5 Named or Concurrent User

licenses

LifeScope™ServerSoftwaretechnicalsupport**

Technical support included in the license fee for the term of the license

LifeScope™ServerSoftwareupdates Patches and updates included in the license fee for the term of the license

Hardwarewarranty* 3-year limited warranty  

Hardwaresupportoptions 3-year Next Business Day worldwide on-site parts replacement service

Hardwarespecifications • Single-node, 48-core/2.1 GHz AMD Opteron 6172 processor

• 96 GB RAM total• Compute cache: 4 x 1 TB drives, RAID 0• Local storage: 5 x 2 TB drives, RAID 5

(7.4 TB usable storage)• Optical drive: DVD-RW internal• Dual power supplies

• 4-node, 48-core/2.66 GHz Westmere X5650 processor cluster configuration

• 24 GB RAM per node• Compute cache per node: 2 x 1 TB drives, RAID 0• Local storage: 6 x 2 TB drives, RAID 5

(9.5 TB usable storage)• 6 Gbps backplane• Cluster private network: QDR (40 Gbps)

Infiniband; IPolB

Operatingsystem 64-bit CentOS 5.x 64-bit CentOS 5.x

Jobscheduler PBS Torque 3.0 and Maui 3.3.1 PBS Torque 3.0 and Maui 3.3.1

Powerinformation • AC input voltage: 180–240 VAC• Rated input current: 7.2 A (180 V) to 9.5 (240 V)• Rated input frequency: 50–60 Hz

The cluster works with 200–240 V and 20 A power; fans are located in the back of each server unit (head node has two fans, and the compute nodes have one fan each)

Powerusage Workstation features a redundant (two separate power modules) 1,400 W high-efficiency power supply

Power usage/heat load information: • Head node: 450 W• Compute nodes: 2 x 700 W = 1,400 W• Switch and LCD: 300 W• Total: 2,150 W or ~7,336 BTU/hr or 0.61 tons AC

Plugtype Standard US three-prong power cable or appropriate country-specific power cable

1 x L6-20 for the compute nodes, 1 x 5-20 for the UPS powering the head node, network, and storage (differs based on country)

* provided by penguin computing. ** provided by Applied Biosystems.1. Specifications subject to change. 2. Renewals of the LifeScope™ Server Software may occur independently from the length of the Workstation or cluster hardware Support; e.g., if the LifeScope™ Server Software is initially purchased for 1 year and the Workstation Support is purchased for 3 years, the LifeScope™ Server Software would have to be renewed twice during the term of the Workstation Support in order to continue data analysis.

Learn more about LifeScope™ Genomic Analysis Solutions at appliedbiosystems.com/lifescope

lifetechnologies.com

Table3.SpecificationsforLifeScope™Cloud.

LifeScope™ Cloud specifications1

Systemcomponents • LifeScope™ Server Software available as an online service

• Individual, secure online account to access software and data

Monthlysubscription • Virtual login node• 1 core, Xeon 5420, 2.4 GHz• 2 GB RAM• 900 GB data transfer/month

• 3,000 core hours per month, with 30-day rollover • 3 TB permanent disc storage• Additional core hours and data transfer available

Technicalsupport3 • Ongoing support for LifeScope™ Server Software and other issues2

• Access to Customer Support Portal • Access to job and billing summary information

1. Specifications subject to change. 2. Subject to maximum combined 4 hours per month for account maintenance and support. 3. provided by penguin computing.