INVIEW DE NOVO GENOME 2.0

SKU#B10140812

Revolutionary, cost-effective genome assembly

INVIEW DE NOVO GENOME 2.0 is suitable for sequencing novel genomes up to 15 Mb in size.  Improved performance with cutting-edge SMRT® technology on PacBio RS II yields effective savings of up to 45% on de novo sequencing of prokaryotic or small eukaryotic genomes. The product facilitates the generation and bioinformatics analysis of exceptionally long reads, resulting in very few contigs, minimal misassemblies and, consequently, truly “(r)evolutionary” genome assemblies.

Highlights of INVIEW DE NOVO GENOME

  • Genome finishing, often with a single contig
  • Complete genome assembly by a non-hybrid approach
  • Assemblies at a finished quality of 99.99% accuracy
  • No gaps, despite using a single sequencing library

Service required

Pre-sequencing

Additional Bio-IT

INVIEW DE NOVO GENOME 2.0

INVIEW DE NOVO GENOME 2.0

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Product Details

Product Details

The full-service package offered by INVIEW DE NOVO GENOME includes

  • Precise de novo genome sequencing based on ultra-long sequencing reads
  • Library preparation with size selection based on BluePippin System
  • Exceptionally long N50
  • Minimal sequencing bias
  • Resolution of low-complexity sequences
  • Bioinformatics analysis that reduces errors in genome finishing based on hierarchical genome assembly (HGAP) approach
  • Perfected for prokaryotic genome assembly, other small genomes
  • Applicable to plant genomes
  • Resolution of entire genome at a very low cost
  • Genome annotation (optional)
  • Base-modification analysis at single-base resolution from the same data set (optional)

Accepted starting material for INVIEW DE NOVO GENOME

  • At least 8 µg of double-stranded, purified, high-molecular-weight, RNA-free DNA
  • DNA isolation from various sources available as an additional service

Please note that only S1-classified material is accepted for RNA isolation ordered online. More information about the current rules for classifying biological material can be found here. Please contact us for further information on isolating RNA from material classified as S2.

Sequencing platform used for INVIEW DE NOVO GENOME

  • PacBio (average genome coverage 100x)

Bioinformatic analysis included in INVIEW DE NOVO GENOME:

  • 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 of INVIEW DE NOVO GENOME:

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

Delivery time depending on project size:

  • INVIEW De Novo Genome 2.0: genome size < 5 Mb
    • 30 days for up to 8 samples
    • 40 days for 9-24 samples
    • Express available
      • 20 days for up to 8 samples
      • 30 days for 9-24 samples
  • INVIEW De Novo Genome 2.0: genome size 5.1 - 10 Mb
    • 35 days for up to 8 samples
    • 45 days for 9-24 samples
    • Express available:
      • 30 days for up to 8 samples
      • 35 days for 9-24 samples
  • INVIEW De Novo Genome 2.0: genome size 10.1 - 15 Mb
    • 35 days for up to 8 samples
    • 45 days for 9-24 samples
    • Express available:
      • 30 days for up to 8 samples
      • 35 days for 9-24 samples

Optional additional Bio-IT for INVIEW DE NOVO GENOME:

  • 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)

Additional Information

Our pre-designed Sequencing Solution simplifies and improves the efficiency of an entire sequencing and microbial genome assembly project, reducing the time and cost of manual assembly curation.

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

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 and sequencing can be carried out simultaneously, permitting an even deeper understanding of functional processes and the phenotypic variability of an organism.

Typical applications for INVIEW DE NOVO GENOME include:

  • Closing genomic sequence gaps to achieve fully resolved genomes
  • Revealing structural variants for functional studies
  • Detecting linked variants that go undetected by short reads
  • Investigation of chromosome structure, repetitive elements, population variation
  • Separating individual genomes from a metagenome
  • Exploring metabolic pathways
  • Genome comparison
  • Improving strains and increasing production rate
  • Simultaneous analysis of epigenetic markers without bisulfite treatment

FAQs

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 in "Files".
 
2. What coverage should I use?
Internal tests showed that a coverage of about 25-30x with corrected PacBio RS II reads is sufficient for producing high-quality genome assemblies. This corresponds to likely raw data coverage of approx. 100x. Assembly results depend in large part on the composition of the analysed genome and may vary between different organisms.
 
3. What starting material should I send and how much of it?
For sequencing on the PacBio RS II,  using high-quality DNA as starting material is crucial. The use of too little, degraded, contaminated or otherwise damaged starting material can result in a low yield or sample preparation failure and impair the quality and quantity of sequencing results. For optimum results, we require at least 10 µg of double-stranded, purified, high-molecular-weight, 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 taking all read information into account, and using optimised 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, as well as the quality of the provided starting material. We therefore 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. Further quality controls are performed at various steps of the process.

6. Do you have any examples of successful joint ventures?
INVIEW DE NOVO GENOME 2.0 was applied within the KLEBSICURE Consortium, a cooperative 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. Arsanis Biosciences GmbH (Vienna, Austria) led the consortium.
The unique combination of de novo sequencing and the detection of base modifications was used to study the virulence of the pathogen, to guide the generation of monoclonal antibody therapies,  and to establish a test method for clinical diagnostics.
 
7. Where should I send my samples?
Please post your samples to:
GATC Biotech AG
European Genome and Diagnostics Centre
Jakob-Stadler-Platz 7
78467 Konstanz
Germany
 
Please do not use GATC Collection Points for shipping NextGen samples, because this will delay sample arrival at the appropriate destination!

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