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(DE) +49 (0) 7531 81 60 68

(FR) +33 (0) 97 04 46 743 

(GB) +44 (0) 207 691 4921

(SE) +46 (0) 8 655 3609

 

customerservice@gatc-biotech.com

 

Opening hours:
8 am - 6 pm CET (Mon-Fri)

Useful downloads

 

FAQ InView De novo Genome 2.0 (PDF, 410 KB)

 

Further reading

 

The advantages of SMRT sequencing, Genome Biology:

http://www.ncbi.nlm.nih.gov

http://genomebiology.com

 

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data, Nature Methods:

http://www.ncbi.nlm.nih.gov

http://www.nature.com

Sequencing technologies


GATC has all the leading sequencing technologies available...more

InView™ De novo Genome 2.0

Revolutionary genome assembly at lowest cost ever!

 

This approach is especially suitable for small genomes. Improved performance with cutting-edge SMRT® Technology PacBio RS II allows an effective saving of up to 45% on de novo sequencing of prokaryotic or small eukaryotic genomes.

Latest technology used for InView™ De novo Genome 2.0 facilitates the generation and bioinformatics analysis of ultra-long reads resulting in fewest contigs, minimum number of mis-assemblies and consequently in really “(r)evolutionary” genome assemblies! 

       

  • Ideal for small genomes
  • Highest N50
  • Fewer and larger contigs
  • Minimum number of mis-assemblies
  • Extremely long read lengths 
  • Genome finishing at lowest cost ever
  • Facilitates detection of structural variants for functional studies
  • Unique! Modification Analysis: Detection of various base modifications in the genome of interest possible   

       

Please choose your required service package

InView™ De novo Genome 2.0



Overview

Determining the complete genome sequence of an organism can be a long and complex approach. InView™ De novo Genome 2.0 simplifies and improves overall efficiency of an entire sequencing and microbial genome assembly project, reducing time and cost for manual curation of the assembly. 

 

Bioinformatic analysis of the ultra-long PacBio RS II reads is based on an algorithm called hierarchical genome-assembly process (HGAP). This new workflow uses multiple alignments of all reads for error correction resulting in highly accurate reads. The following assembly delivers a most complete and accurate de novo genome sequence in which even long repeat regions are successfully resolved.

 

This optimised approach enables academic and industrial researchers to identify the genetic basis for certain metabolic pathways and to characterise the functional potential of microorganisms. The information can be used to improve industrial processes, for example in the production of feed, food, paper or energy (White Biotechnology).

 

InView™ De novo Genome 2.0 also offers the unique opportunity to go beyond the information encoded in the DNA sequence by gaining additional epigenetic information. Modification analysis can be done simultaneously with sequencing, allowing an even deeper understanding of functional processes and the phenotypic variability of an organism.

  

High-quality finished genomes are crucial for:

  

  • Characterising the functional potential of microorganisms
  • Discover, analyse and understand metabolic pathways
  • Comparing genomes
  • Improving strains and increasing production rate

   

Service & Specification

InViewTM De novo Genome 2.0 with PacBio RS II Technology

 

Complete all-in-one service includes:   


  • Library preparation and sequencing
  • Bioinformatics based on HGAP workflow for superior genome assembly 
  • Barcode labeling of samples by the customer and automated LIMS-controlled workflows at GATC Biotech allow unambiguous sample identification and real-time tracking of the entire sequencing project via your secured online account myGATC
  • Available with ISO 17025 service standard on request

 

Optional: 

  • Genome annotation

 

Starting material: High-quality genomic DNA 

 

Sequencing platform: SMRT® Technology PacBio RS II

 

Average genome coverage: 100x

 

Bioinformatic analyses: 

  • Quality filtering of PacBio RS II reads
  • Improvement of long PacBio RS II reads through alignment of short reads („read of insert“)
  • Assembly of long high-quality reads
  • Assembly correction

 

Deliverables:

  • PacBio RS II raw data (fastq, bas.h5, metadata.xml)
  • Consensus sequence of assembled contigs (fasta)
  • Assembly statistics (pdf)

 

Delivery time: approx. 4 weeks. Express delivery on request.

 

Optional additional services: 

  

Genome annotation:

  • Gene detection
  • Functional assignment
  • EC number assignment
  • CAZy number assignment


Deliverables:

  • Annotated sequences (Excel and GenBank format)


Base Modification Analysis:

  • Mapping of raw reads against de novo assembled contigs
  • Analysis of the polymerase kinetics during sequencing
  • Detection of potentially modified bases

   

Deliverables:

  • Filtered subreads (fasta)
  • Alignment file (bam)
  • Coverage report (bed)
  • Consensus sequence (fastq)
  • Table of detected modifications (csv, gff)

        

Expertise

The KLEBSICURE Consortium

InView™ De novo Genome is applied for the KLEBSICURE Consortium, a cooperation project with GATC Biotech AG, the Max Planck Institute for Infectious Biology (Berlin, Germany) and the Ludwik Hirszfeld Institute of Immunology and Experimental Therapy (Wroclaw, Poland) as consortium members and Arsanis Biosciences GmbH (Vienna, Austria) as consortium leader. 
  
Main objective of the project is the identification and characterisation of the pathogen Klebsiella pneumoniae which causes severe infections. The unique combination of de novo sequencing and detection of base modifications is used to study the virulence of the pathogen to guide the generation of monoclonal antibody therapeutics and to establish a test method for clinical diagnostics.

    

FAQ & Demodata

1. Where do I get my results?

All raw data as well as the analysed and assembled data can be downloaded via your secure myGATC online account. Example data of de novo assembly of E. coli DH1 can be viewed after login

 

ecoli_dh1_hgap_assembly_6smrtcells.png 

ecoli_dh1_hgap_assembly_6smrtcells_20Kb_contigs.fas

ecoli_dh1_hgap_assembly_6smrtcells_demo.pdf

 

2. What coverage should I use?

Internal tests showed that a coverage of about 25-30x with corrected PacBio RS II reads is sufficient to produce high-quality genome assemblies. This corresponds to a raw data coverage of approx. 100x that should be achieved. Assembly results highly depend on the composition of the analysed genome and may vary between different organisms. 

 

3. Which and how much starting material should I send?
For sequencing on the PacBio RS II it is crucial that high-quality DNA is used as starting material. The use of too little, degraded, contaminated or otherwise damaged starting material can result in low yield or failure of the sample preparation and impair quality and amount of sequencing results. For optimal results we require at least 10 µg double-stranded, purified, high molecular and RNA-free DNA (concentration approx. 200 ng/µl; OD 260/280 ≥ 1.8; OD 260/230 ≥ 1.9).

 

4. Do you guarantee a certain output?
Sequence data are assembled de novo under consideration of all read information, using optimized programs and parameters. The number of contiguous sequences (contigs) that can be unambiguously assembled depends on the complexity (frequency, length and distribution of highly repetitive and duplicate regions) of the sequenced genome and also the quality of the provided starting material. Therefore we cannot guarantee a minimum number of contigs.

 

5. What kind of quality controls do you perform?
The quality and quantity of each incoming sample will be determined by appropriate methods (e.g. agarose gel analysis / Qubit® Fluorometer / NanoDrop / Agilent 2100 Bioanalyzer). Further quality controls are performed at various steps of the process.

 

6. Where should I send my samples?
Send your samples by post to the following address:

 

GATC Biotech AG

European Genome and Diagnostics Centre

Jakob-Stadler-Platz 7

D-78467 Konstanz, Germany

Copyright © 2014 GATC Biotech AG. All rights reserved.
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