Leading Edge Genomic Services & Solutions

De Novo Sequencing

Service Overview
Novogene Data
Contact Us

de novo sequencing and de novo assemblyWith de novo  sequencing, the first genome map for a species is generated, providing a valuable reference sequence for phylogenetic studies, analysis of species diversity, mapping of specific traits and genetic markers, and other genomics research.

With the development of next-generation sequencing technology, de novo sequencing has become more rapid and affordable, and Novogene is at the forefront of this technology. Novogene’s founder, Dr. Ruiqiang Li, is a leading genomics expert and a primary developer of the SOAPdenovo software package for genome assembly. Dr. Li and the Novogene team have contributed to several important publications on novel genome sequences, and we can provide you with the high level of expertise required for your specific project.

Novogene offers de novo sequencing services using various platforms including Illumina, PacBio and 10X Genomics. For each project, our scientists will design the best sequencing strategy utilizing an optimal combination of short reads and long range sequence information to achieve the most comprehensive de novo assembly results for your genome of interest.

Project Types

Simple Genome

Simple genome refers to a haploid genome with a low repeat content (less than 50%), or a diploid genome with a low rate of heterozygosity (less than 0.5%), such as most mammals, birds, and cultivated crops.

Complex Genome

Complex genome refers to a diploid or polyploid genome with a high repeat content (higher than 50%) or a high rate of heterozygosity (higher than 0.5%), such as many species of plants, aquatics, and insects.
  • Moderately heterozygous genome (diploid)
  • Highly heterozygous genome (diploid)
  • Highly repetitive genome (diploid)

The Novogene Advantage

  • Highly experienced: We have completed major de novo genome sequencing projects, and our data has been published in top-tier journals.
  • Leader in NGS services: We provide high-quality sequencing, an efficient standard workflow, fast turnaround time, and bioinformatics analyses at a cost-effective price.
  • Bioinformatics expertise: The SOAPdenovoII software and the NovoHeter software, developed by Novogene scientists, are used for complex genome assembly.
  • Diverse strategies: Incorporating sequencing results from various platforms including Illumina HiSeq, PacBio and 10X Genomics, we offer the best assembly solution tailored towards each unique genome.

Project Workflow

de novo sequencing service project workflow

Sequencing Strategy & Data Quality Guarantee


 GENOME SURVEY ANALYSIS
PlatformIllumina
Sequencing Libraries350 bp insertion
Sequencing StrategyHiSeq PE150
 SIMPLE GENOME DE NOVO SEQUENCINGCOMPLEX GENOME DE NOVO SEQUENCING
Assembly Strategy IIllumina short-read-based assembly
Sequencing Libraries250 bp / 450 bp /
2 Kb / 5 Kb / 10 Kb insertions
250 bp / 350 bp / 450 bp /
2 Kb / 5 Kb / 10 Kb / 20 Kb insertions
SoftwareSOAPdenovoIINOVOheter
Data Quality GuaranteeMammal (except Chiroptera) or bird genome:
Contig N50 ≥ 40 Kb
Scaffold N50 ≥ 4 Mb

Other genomes:
Contig N50 ≥ 30 Kb
Scaffold N50 ≥ 1 Mb
Contig N50 ≥ 20 Kb
Scaffold N50 ≥ 500 Kb
Assembly Strategy IIIllumina short-read-based assembly and gap-filling using PacBio long read data
Data Quality GuaranteeMammal (except Chiroptera) or bird genome:
Contig N50 ≥ 80 Kb 
Scaffold N50 ≥ 4 Mb 

Other genomes:
Contig N50 ≥ 60 Kb 
Scaffold N50 ≥ 1 Mb
Contig N50 ≥ 40 Kb
Scaffold N50 ≥ 500 Kb
Assembly Strategy III
(Recommended)
Hybrid assembly integrating Illumina short read data, PacBio long read data,
and 10X Genomics linked read data
Data Quality GuaranteeContig N50 ≥ 500 Kb
Scaffold N50 ≥ 1 Mb
Contig N50 ≥ 200 Kb
Scaffold N50 ≥ 1 Mb
Assembly Strategy IVHybrid assembly integrating PacBio long read data, and 10X Genomics linked read data
Data Quality GuaranteeContig N50 ≥ 1 Mb
Scaffold N50 ≥ 3 Mb
Contig N50 ≥ 500 Kb
Scaffold N50 ≥ 1 Mb

Customized services are also available upon request. Please contact us for more information.

Sample Requirements

  • DNA amount for survey: ≥ 10 µg (quantified by Qubit 2.0)
  • DNA amount for genome de novo sequencing: ≥ 500 µg (quantified by Qubit 2.0)
  • DNA concentration: ≥ 50 ng/μl
  • Purity: OD260/280 = 1.8 - 2.0 without degradation and RNA contamination

Analysis Pipeline

de novo sequencing service analysis pipeline

The following study utilized Novogene's expertise in de novo sequencing and de novo assembly.

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.
Nature Genetics, 46:1303–1310 (2014)

Researchers from Novogene and the Chinese Academy of Science collaborated on the whole-genome sequencing of the golden snub-nosed monkey, a species of Old World monkey. The de novo genome sequencing data were compared with genome resequencing data from three other related species, and provided insights into the evolutionary adaptations associated with the unique diets of these primates.

de-novo-data
Figure. Phylogenetic tree and estimated divergence times for GSM and other mammals.

Novogene Publications

JournalTitle
Nature Biotechnology 33:531 (2015)Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.
Nature Genetics, 46:1303 (2014)Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.
Nature Biotechnology, 32:1045 (2014)De novo assembly of soybean wild realtives for pan-genome analysis of diversity and agronomic traits.
Nature Genetics, 45:1431 (2013)Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars.
Nature Communications, 4:2071 (2013)Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.
  Whole Genome Sequencing on HiSeq X (Human/ Animal/ Plant)
  Whole Exome Sequencing
  mRNA-Seq
  LncRNA Sequencing
  Small RNA Sequencing
  Whole Genome Bisulfite Sequencing
  ChIP-Seq
  Animal & Plant Re-Sequencing
  Genotyping by Sequencing
  de novo Sequencing
  Pan-genome Sequencing
  Metagenomic Sequencing
  Single-cell DNA Sequencing
  Single-cell RNA Sequencing
  16S/18S/ITS Amplicon
  Others- please specify
  Human
  Others