INVIEW De Novo Genome

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.

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

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

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 same data set (optional)

Accepted starting material for INVIEW De Novo Genome

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

Please note, that only S1-classified material is accepted for DNA isolation ordered online. More information about current classification of biological material can be found here (TRBA 466). Please contact us for further information on DNA isolation from material classified as S2.

Sequencing platform: PacBio (average genome coverage 100x)

Bioinformatic analysis

• 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 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

• Genome annotation
  • Gene detection
  • Functional assignment
  • EC number assignment
  • CAZy number assignment
• Deliverables
  • Annotated sequences (Excel and GenBank format)
• 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 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, 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 with, permitting an even deeper understanding of functional processes and the phenotypic variability of an organism.