CLCGenomics

Workbench
Features & Bene ts

Solving the data analysis challenges of

Next Generation Sequencing As all other Workbenches from CLC bio, CLC Genomi
Director of the Einstein
Workbench runs on Mac OS X, Windows, and Linux pla
Center for Epigenomics at
With
the Albert Einstein College
Next Generation Sequencing machines,
forms. High
You decide which computer to run your softw
Throughput
of Medicine, Dr. John Gre- Sequencing has become accessible
on – to a very
not us.
ally, states: large group of researchers. However, data analysis repre-

-
CLC bio's tools are go- Some features of CLC Genomics Workbench
turn of Investment of current NGS investments.
ing to put sophisticated
Genomics
analytical ability intoCLC Genomics Workbench solves this problem and will
ference assembly
the hands of molecularenable everyone to rapidly analyze and visualize the of Sanger, 454, Illumina Genome
biologists at Einstein, Analyzer, SOLiD, and Helicos sequencing data
huge amounts of data generated by NGS machines. The
and will greatly enhance Assembly of genomes of any size (only
AM limited by
user-friendly and intuitive interface essentially
available) takes
de novo
assembly of genomes up to 50
their ability to explore
High Throughput Analysis from hardcore bioinformatics
mega-bases
the massively-parallelprogrammers doing command-line scripts, to Color
researchers
space assembly
sequencing data that Advanced visualization, scrolling, and zooming tools
and scientists searching for biological results. Further-
we are generating. We SNPWorkbench
detection using advanced statistical models
more, the versatile nature of CLC Genomics
see this as a way of Support for multiplexing with DNA barcoding
allows it to blend seamlessly into existing sequencing
Detection of large-scale genomic events
lowering barriers for
analysis work ows, easing implementation and maximiz-
scientists who have not Transcriptomics
previously performed ing return on investment.
these high-throughput A-seq
epigenomic assays, al-Multi technology – multi platform EST library construction
Advanced visualization, scrolling, and zooming tools
lowing them to explore
CLC Genomics Workbench includes High Gene expression analysis
Performance
their data and explore
hypotheses. Computing accelerated assembly of Next Generation
ClassicalSe-sequence analysis tool s
quencing data as well as support for a large number of
downstream analyses. Primer design
Molecular cloning
BLAST
CLC Genomics Workbench is the rst comprehensive
ME anal-
ysis package which can analyze and visualize
Alignmentsfrom
data
Version 3.1 for Windows, all major NGS platforms, such as SOLiD Phylogenetic
from Applied Bio-trees
Mac OS X, and Linux Adva NA structure prediction and editing
tegrated 3D molecule analysis
CLC bio©Copyright 2009 Analyzer from Illumina, and HeliScope from Helicos. Col-
Secondary protein structure predictions
laboration with the instrument vendors is And
a natural part
much more
of CLC bio’s development process.

clcbio.com

CLC Genomics Workbench / 1

Genomics Features
CLC bio’s world renowned scientists have designed completely new and inno-
vative algorithms to power the features of CLC Genomics Workbench. These
highly advanced and cutting edge algorithms incorporate SIMD processor
accelerating technology to yield a significant speed-up of the reference as-
sembly as well as the de novo assembly processes.
Support for analysis of hybrid data
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de novo assembly support the analysis of dif-
ferent kinds of data at the same time. An example could a de novo assembly
of Sanger data, 454 singe read data, and Illumina paired end data in the
same analysis.

This functionality dramatically reduces manual work for the scientists, fa-
cilitating focus on deriving biological results from the data instead of doing
tedious data-crunching.

Multiplexing
Assembly view, zoomed out, together with a sequence view showing de-
tails of the contig sequence. A region of low coverage has been found in When doing batch sequencing of different samples, you can use multiplexing
the assembly view, and the corresponding region of the contig sequence is techniques to run different samples in the same run. There is often a data
automatically highlighted in the sequence view. analysis challenge to separate the sequencing reads, so that the reads from
one sample are assembled together.
Reference assembly / mapping
CLC Genomics Workbench support a large number of
The reference assembly functionality of CLC Ge- CLC Hardware multiplexing protocols for various types of mul-
nomics Workbench supports both short and Bioinformatics Processing tiplexing based on name and multiplexing
long reads, it supports paired-ends reads, Database Units based on tags or barcoding.
it supports gapped and ungapped align-
ments, and it supports Sanger, 454, Il- CLC Storage SNP detection
lumina Genome Analyzer, Helicos, and Science System CLC Genomics Workbench offers auto-
SOLiD sequencing data. Server (incl. hardware) mated SNP detection (see our Bioin-
formatics explained article on SNPs at
CLC Genemoics Workbench can as- CLC Genomics IUUQXXXDMDCJPDPN#&

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semble genomes of any size as long as CLC Workbench Training detection in CLC Genomics Workbench
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Performance Features &
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formance computing based algorithm. Up to 80% more tion will also report whether the SNP is synonymous or non-
hits have been shown when assembling 35 mer SOLiD data in color synonymous. If the SNP variant changes the amino acid in the protein
space, compared to assembling the same data in base space. translation, the new amino acid will be reported.

De novo assembly
The de novo assembly of CLC Genomics Workbench supports both short and
long reads, it supports paired-ends reads, and it supports Sanger, 454, Il-
lumina Genome Analyzer, Helicos, and SOLiD sequencing data.
The de novo assembly process has two stages: First, contig sequences are
created by aligning all the reads. Second, all the reads are assembled using
the contig sequence as reference.
Depending on the coverage of the data, the data type, and the species, CLC
Genomics Workbench de novo assembles genomes of up to 50-100 mega
bases in size.
The graphical user interface allows the user to easily identify SNPs and get a
graphical overview of SNPs in smaller or larger genomic regions.
Identifying genomic rearrangements
Through advanced graphical user interface, CLC Genomics Workbench sup-
port the identification of a variety of genomic rearrangements like insertions,
deletions, duplications and inversions.
Transcriptomics Features
CLC Genomics workbench has tools to support a full work flow in analysis
of single-color microarray gene expression data. These include visual quality
control tools, such as principal component blots and box plots, transforma-

2 / CLC Genomics Workbench

tion and normalizations tools, tools for statistical testing and false discovery designed to verify putative exons transcripts:
rate control,  clustering algorithms, heat-map visualization, and tests on
gene annotations, such as Hyper Geometric tests and Gene Set Enrichment EST library contruction
analysis. EST library can be constructed using the de novo assembly algorithm - e.g. to
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The interactivity of the multiple available views, allows easy navigation and ics.
overview of data and analysis results. The complete integration of the ex-
pression analysis in the workbench enables the user to carry out downstream
analysis of genes of interest with the comprehensive set of sequence analysis
tools provided, immediately and without the hassle of switching between
softwares.

Digital Gene Expression

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and easy way for normalizing values for the expression level of a gene when
Classical Sequence Analysis
using Digital Gene Expression.
In addition to all the Next generation Sequencing analysis tools, CLC Genom-
Feature ID Expression Transcripts Unique Unique Total gene reads
values gene reads exon reads ics Workbench include all the more than 100 features of CLC Main Workbench
ABHD8 5.416,87 1 656 595 695
for carrying out downstream analysis and for designing follow-up lab experi-
ABHD9 21,02 1 18 2 32
AKAP8 673,58 1 222 124 361 NFOUT
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AKAP8L 4.311,30 1 772 478 897 5 different types of alignments, phylogenetic analyses.
ANKRD41 125,49 1 27 20 31
AP1M1 2.749,13 1 426 326 468
ARMC6
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1.034,80
1
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236
149
160
230
333 Database Integration
ATP13A1 1.332,95 1 325 244 341
B3GNT3 0,00 1 36 0 76 CLC Genomics Workbench is fully integrated with CLC Bioinformatics Data-
BRD4 1.427,11 2 656 554 693
BST2 1.479,23 1 67 60 80
base, supporting Oracle, MySQL, PostgreSQL, H2, and Microsoft SQL Server.
C19orf42 720,63 1 91 51 107 This enables all users to share and search data in a flexible, secure, and very
C19orf44 943,97 1 92 13 316
C19orf50 2.653,11 1 264 195 307
user-friendly environment.
C19orf60 5.254,14 2 346 242 359
C19orf62 3.789,73 2 378 288 428
CALR3 0,00 1 47 0 90 Server Integration
CASP14 0,00 1 5 0 7
CCDC105 0,00 1 14 0 16
CLC Genomics Workbench integrates smoothly with CLC Genomics Server.
CCDC124 5.040,96 1 320 274 342
CHERP 1.668,09 1 239 172 474 This enables the Genomics Workbench user to run heavy jobs like whole ge-
CIB3 0,00 1 25 0 44 nome assemblies on a central, powerful, computer while working with down-
CILP2 31,72 1 9 7 10
COMP 124,16 1 29 16 35 stream analyses of other data on the local computer.
COPE 7.315,62 3 582 429 649
CPAMD8 98,50 1 280 31 553
CRLF1 881,29 1 116 83 145
CRTC1 3.396,18 2 1613 1244 1790
CYP4F11 193,77 1 50 31 58
CYP4F12 33,09 1 44 2 76
CYP4F2 8,06 1 3 0 9

A table view of an expression sample generated from a sequence file of

NGS mRNA reads.

Discovery of novel transcript variants

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ering putative exons (intronic regions containing a relative high number of
matches). This could indicate that this region is present in a novel transcript In additionto computational power, CLC Genomics Server offers a flexible job
variant. Using existing primer design tools in the Workbench, primers can be queuing system, easy integration with other applications, easy data sharing

CLC Genomics Workbench / 3

opportunities., and a range of other functionalities Import formats
to ensure that your Next Generation Sequencing
analyes are carried out in a fast, secure, and flexible
IT environment.

Customization
A new and fast evolving technology, Next Generation
Sequencing constantly provides researchers with
new scientific opportunities and new ways of ana-
lyzing the huge amounts of data.

The problem is not lack of ideas or lack of data. The

problem is lack of efficient software for carrying out
the analyses or for removing manual bottlenecks in
the workflow.

CLC bio eliminates these challenges by offering a

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algorithms with our products.

We also design and develop customized add-on

modules for CLC Genomics Workbench and CLC Ge-
nomics Server based on specific customer requests.
This is a quick and cost effective way of improving
both the speed and the quality of your research.

System requirements
Ŧ
Mac OS X 10.4 or later (including Intel-based Macs)
Ŧ
Windows 2000, Windows XP, or Windows Vista
Ŧ
Linux:
3edhat or SuSE
Ŧ
32 bit version and 64 bit versions of operating system on all platforms
Ŧ

(#
3AM required
Ŧ

to 16 GB required for large assemblies
Ŧ

Y
768 display recommended

Contact your local sales representative or send

an e-mail to sales@clcbio.com if you would
like to try CLC Genomics Workbench.

CLC bio · Finlandsgade 10-12
Katrinebjerg · DK-8200 Aarhus N
Denmark
Phone: +45 70225509
www.clcbio.com · info@clcbio.com
CLC bio LLC · 245 First Street · Suite 1826
Cambridge, MA 02142
USA
Phone: +1 (617) 444-8765
www.clcbio.com · info@clcbio.com

4 / CLC Genomics Workbench