Chun lab company introduction

www.chunlab.com

Copyright 2014 ChunLab, Inc.ⓒ

ChunLab Company Introduction

Contents

2BIOINFORMATICS MADE EASY CHUNLAB

| About ChunLab| Why ChunLab| ChunLab Services

About ChunLab

BIOINFORMATICS MADE EASY CHUNLAB 4

About ChunLab

• ChunLab is a next-generation sequencing (NGS) and bioinformatics service provider offering an end to end solution from sample to discovery

• Established in Dec. 2009 by Professor Jongsik Chun of Seoul National University

• Headquarters in Seoul, Korea with a satellite office in Rockville, MD


Our Mission

ChunLab’s mission is to simply bioinformatics to give clients control over their NGS data

To achieve this mission, we have designed optimized analysis pipelines forvarious research disciplines (metagenomics, genomics and transcriptomics)using carefully chosen, tested algorithms and biostatistical techniques.

Furthermore, we have designed a suite of point and click software tools thatenable researchers to easily perform sophisticated visualizations, secondaryanalysis and comparative analysis.


Professional career– Full Tenured Professor, School of Biological Sciences,

Seoul National University (SNU) (2000~Present)– Senior Researcher, Korea Research Institute

of Bioscience and Biotechnology (KRIBB)– (1998~2000) – Research Associate, University of Maryland,

USA(1996~1998)

– Associate Editor, IJSEM (2002~2014)– Editorial Board , A Van Leeuw. J. Microb. (1999~present)

Microb. Environ. (2005~Present)– Founding Director, Bioinformatics Institute,

Seoul National University (2010).

About Dr. Jongsik Chun, CEO of ChunLab

Why ChunLab?


Why ChunLab?

Intuitive point & click user interfaces with advanced visualization and analytical tools

Standalone Windows and MAC based applicationsData results provided in sophisticated publication ready visualizationsExportation of data into Excel, text or FASTA formats for further downstream

analysesNo expertise in PERL, Python, C, C++ required

CLcommunityTM

for Microbial Community Analysis

CLgenomicsTM

for Whole Genome Analysis

CLRNASeqTM

for Transcriptomics Analysis

Suite of software tools designed for specific research disciplines


List of highly curated proprietary reference databases

EZTaxon

EZGenome

EZFungi

• Database of 16S rDNA sequences of species type strains for valid and invalid names• 63,000+ 16S rRNA gene sequences for Bacteria & Archaea (Nov 2014)• 9,900 users world wide• >2,600 citations

• Database of manually curated prokaryote genomes• > 25,000 prokaryote genomes as of Nov 2014

• Database of highly curated fungal strains using the ITS region• >17,000 fungi species as of Nov 2014

Why ChunLab?

For more information visit us at http://www.ezbiocloud.net

EZRNASeq • Need description to be launched?????

EZEcology • Need description to be launched?????


Composed of Ph.D. and master level bio scientists, bioinformatics specialists and software developers

Why ChunLab?

To provide…

• Consultation on the best platform(s) and study design for a success research project

• NGS and bioinformatics training (through workshops and webinars)


Equipped with State-of-the-Art Facilities and NGS Platforms

Why ChunLab?


Why ChunLab?

Over 400 government and research agencies, medical centers, companies and universities using ChunLab’s services worldwide


What Our Clients Are Saying

It has been a pleasure working with ChunLab. At every step of the way, ChunLab members assisted with shipping/customs, sample preparation, and data generation. Their knowledge of microbial systems, in particular, sets this group apart from other genomic facilities. The resulting publication would not have been possible without the extra input and analysis of results by ChunLab team members.

Dr. Shana K. GoffrediAsst. Professor | Occidental College (USA)

”“

We are very happy with the genome sequencing and analysis results ChunLab provided us with and we would certainly recommend ChunLab to our colleagues. I do not have any genome-sequencing projects planned for next year, but ChunLab will definitely be my first choice when I next want a bacterial genome sequenced.

Dr. Paul MeyersProfessor | Dept of Molecular & Cell Biology, Univ of Cape Town

”“

Yes I was able to download all the software and use it to analyze my data. It is very user-friendly. Overall we are very satisfied with your service and quality of the data. ”

“Dr. Jing WangResearcher | Instit. of Molecular and Cell Biology (Singapore)

ChunLab ServicesMicrobiome / Microbial Community Analysis


Microbiome/Microbial Community Analysis

• ChunLab provides a full service solution for microbiome / microbial community analysis using the 16S rRNA gene (bacteria and archaea) and the ITS region (fungi)

• Service includes: Library preparation, sequencing on Roche 454 or Illumina MiSeq platforms, comprehensive data analysis, and the delivery of results via our easy to use software browser, CLcommunity

• Bioinformatics only services also available


ChunLab’s Microbial Community Bioinformatics Pipeline*

Remove chimeric sequences

Taxonomic assignment using the EzTaxon and EzFungi databases**

Cluster reads for de-noising

Trim primers using pairwise alignment and the Hidden Markov Model

Paired end merge

Filter low quality sequences

Calculation of diversity index using various statistical analyses

Creation of CLC format files to be viewed in CLcommunity

*Above pipeline is for MiSeq generated data. Processing steps may vary for 454 generated data or change according to client requests and need**ChunLab provides superior phylogenetic identification and taxonomic assignment using our own highly curated in-house databases.

YJEON

sorting of barcode is not necessary in this case thus "Paired end merge" should be enough.In the fixed pipeline, "Filter low quality sequences" is perfomred firstly, so this step should be moved to the top.


CLcommunityTM

CLcommunity is our most versatile and easy-to-use software package specially created for the purpose of visualizing next generation sequenced (NGS) data to identify and quantify species within a given microbial community.

Software Highlights:

• Free software that reads only CLC (ChunLab Community) formatted files that are generated

through ChunLab’s analysis pipeline

• ChunLab’s analysis pipeline can analyze NGS data generated from any platform

(454, MiSeq, Ion Torrent, etc)

• Ability to browse and compare up to 100 samples simultaneously

• Analyses available: taxonomic compositions as bar, pie or KRONA charts; microbial source

tracking; clustering heat maps; rarefaction curves; rank abundance; diversity indices; taxonomic

exclusivity analysis, Canonical Correspondence Analysis (CCA); Fast Unifrac Analysis; BLAST

searches


CLcommunity for Microbial Community Analysis

Main Browser Interactive taxonomic composition chart

Taxonomic composition as a pie chart with ability to view changes in time series data

Krona Chart


CLcommunity – View Taxonomic Similarity in Heat MapsHeat Map Rarefaction Curve

Canonical Correspondence Analysis (CCA) Diversity Indices

ChunLab Services

RNA Sequencing Analysis


RNA Sequencing Analysis

• ChunLab provides a full service solution for RNA Sequencing analysis (bacteria, human, mouse, etc)

• Service includes: Library preparation, sequencing on Illumina HiSeq 2500, comprehensive data analysis, and the delivery of results via our easy to use software browser, CLRNASeq



CLRNASeqTM

Our suite of robust CLRNASeq solutions is developed for discovering, profiling and quantifying RNA transcripts. Each CLRNASeq software solution has an intuitive interface with point and click menu options that give users the power to browse mRNA mappings easily.

Software Highlights:• Free software that reads only CLT (ChunLab transcriptomics) and CLG (ChunLab Genome) formatted files that are

generated through ChunLab’s analysis pipeline

• ChunLab’s analysis pipeline can analyze NGS data generated from any platform

• Can browse and compare up to 20 samples simultaneously

• Analyses available: gene expressions analysis, differentially expressed genes; clustering of gene sets with similar

expression patterns; KEGG and eggNOG metabolic pathway analysis; SNP / InDel analysis; expression profiling;

normalization using RPKM , RLE and TMM algorithms


CLRNASeq for Transcriptomics AnalysisTranscript gene expressions mapped to

reference genome Differential Expression Gene Analysis

KEGG Metabolic Pathway Analysis Read Normalization using RPKM, TMM and RLE


CLRNASeq for Transcriptomics Analysis

SOM

Hierarchical

K-Means

Choose from 3 different clustering methods

ChunLab ServicesMicrobial Genome Analysis


Microbial Genome Analysis

• ChunLab provides a full service solution for Microbial Genome Analysis (Bacteria, Fungi, Virus, etc)

• Service includes: Library preparation, sequencing on Illumina MiSeq or PacBio, data analysis (assembly, annotation and gene by gene genome comparisons); and the delivery of results via our easy to use software browser, CLgenomics

• Bacterial genomes present in our academic database (EzGenome) can also be freely visualized and analyzed in our CLgenomics software (for more information visit wwww.ezbiocloud.net)



CLgenomicsTM Genome Browser

CLgenomics is a powerful desktop application

specifically designed to deliver insights into

microbial genomes at the click of button.

3 Main Functions of CLgenomics:

1) Multiple genome browser – easy gene finding, explore gene functions, view COG distributions and other

detailed statistics: coverage, GC ratio, genome size, contigs (N50), scaffold, CDS, etc.

2) Analytic tool -- comparative genome analysis and BLAST searches

3) Data transformer – instantly creates reports and graphs such as circular genome mappings (rRNA, tRNA, CDS,

GC ratio, GC skew); exports raw sequence data and statistics as Excel, Word, FASTA, GenBank formats or files

for NCBI submission

NOTE:

• CLgenomics can only view CLG (ChunLab Genomics) and CG (Comparative Genomics) format files that are generated through

ChunLab’s bioinformatics pipeline


CLgenomics for Microbial Genome Analysis

Genome Mapping

Genome browsers with simultaneous comparison of several genomes

Gene by gene genomic comparison


CLgenomics for Microbial Genome Analysis

Translation, ribosomal structure and biogenesis, 123

Transcription, 86

Replication, recombination and repair, 92

Cell cycle control, cell division, chromosome partitioning, 17

Posttranslational modification, protein turnover, chaperones, 40

Cell wall/membrane/envelope

biogenesis, 88

Cell motility, 5

Inorganic ion transport and metabolism, 48

Signal transduction mechanisms, 43

Energy production and conversion, 43

Carbohydrate transport and

metabolism, 85

Amino acid transport and metabolism, 59

Nucleotide transport and metabolism, 56

Coenzyme transport and metabolism, 28

Lipid transport and metabolism, 24

Secondary metabolites biosynthesis, transport and catabolism, 5

General function prediction only, 129

Function unknown, 127

Weissella Koreensis JC2156

COG Browser

COG Distribution

COG Distribution Comparison


CLgenomics -- Genome BLAST Function

Genome BLAST function

Export Data for NCBI Submission

Data plot using MUMmer

ChunLab’s Other Services


Physical Genome Mapping based on the Bionano Irys System

The Irys System generates high resolution genome maps of extremely long DNA (hundreds of kbs to more than a megabase long) without amplification, providing long-range contiguity of the genome.

Applications: • Reveal order and orientation of functionally relevant components of complex

genomes• Provide comprehensive SV (structural variation) detection and epigenetic

modifications that NGS misses• Provide reference genome validation, gap sizing and haplotyping• Eliminate re-sequencing bias

Genome maps are delivered via the IrysView Software, where genome map to map comparisons are possible. In addition, NGS contig data can be imported to finish complex genomes, validate NGS assemblies, and detect structural variations


Gene Expression Profiling Based on NanoString Technology

• The nCounter Analysis System from NanoString Technologies offers a simple, cost-effective way to profile hundreds of mRNAs, microRNAs, or DNA targets simultaneously with high sensitivity and precision. • Highly reproducible with no amplification needed

• Ability to probe 800 genes simultaneously

Ideal for:• Formalin-Fixed Paraffin-Embedded (FFPE) samples• Low input volume samples (starting from 100ng or less of total RNA)• Cell or blood lysates

Applications:• Gene expression profiling• Fusion genes• Copy Number Variation (CNV)• Single cell gene expression


For more information visit us at www.chunlab.com or contact us at [email protected]

Korea HQSeoul National University, Bldg 105-1, Suite #307, 1 Gwanok-ro, Gwanak-gu, Seoul, Korea 151-742, Tel: +82-2-875-2501

ChunLab USA9601 Medical Center Drive, Suite 326, Rockville, MD 20850, Tel: +1-240-731-8527

http://www.chunlab.com/

mailto:[email protected]

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