Novogene offers de novo sequencing services using both PacBio and Illumina platforms. We provide multifaceted sequencing services including genome survey, draft map, complete map, and fine map tailored to different research needs. For each project, our scientists will design the best sequencing strategy utilizing an optimal combination of short reads and long-range sequencing information to achieve the most comprehensive de novo assembly results for your genome of interest.
Applications
For individual research：
- Virulence research
- Drug resistance mechanism
- Molecular markers
- Vaccine development
For population research：
- Evolution relationship
- Population size
- Epidemiology
- Microbial evolution
Benefits
Highly experienced: We have completed numerous microbial De novo sequencing projects with 20 publications in top-tier journals.
Largest sequencing capacity: We have the largest Illumina and PacBio sequencing capacity in the world, allowing us to provide high-quality data, fast turnaround, and affordable prices.
n-depth data mining: We have complete solutions for in-depth analysis of individual variations and interpretation of population evolutionary history to solve your biological problems that interest you.
Accuracy: Creates accurate reference sequences, even for complicated or polyploid genomes.
Specifications: DNA Sample Requirements
| Platform Type | Sample Type | Amount (Qubit®) | Purity |
| Illumina
NovaSeq 6000 |
Genomic DNA | ≥ 200 ng | A260/280=1.8-2.0 no degradation, no contamination |
| PacBio Sequel IIe DNA CLR library |
HMW Genomic DNA (Bacteria and Fungus) |
≥ 5 μg (Concentration ≥ 70 ng/μL) |
A260/280=1.7-2.0; A260/230=1.3-2.6; *NC/QC=0.95-3.00 Fragments should be ≥ 20 kb |
| PacBio sequel IIe DNA HiFi library |
HMW Genomic DNA (Fungus) |
≥ 8 μg (Concentration ≥ 70 ng/μL) |
A260/280=1.7-2.0; A260/230=1.3-2.6; *NC/QC=1.0-2.2 Fragments should be ≥ 20 kb |
| Nanopore PromethION | HMW Genomic DNA (Bacteria and Fungus) |
≥ 6 μg (Concentration ≥ 60 ng/μL) |
A260/280=1.7-2.2; A260/230=1.3-2.6; *NC/QC=0.95-3.00 Fragments should be ≥ 20 kb |
* NC/QC: NanoDrop concentration/Qubit concentration
Specifications: Sequencing & Analysis
| Platform Type | Illumina NovaSeq | PacBio Sequel II/IIe System | ||
| Read Length | Paired-end 150 bp | N50>15 kb, long read lengths up to 25 kb（CCS） | ||
| Recommended Sequencing Depth | ≥ 50x for bacterial and fungal genomes | ≥ 100X for bacterial genomes ≥ 50X for fungal genomes | ||
| Data Analysis | Bacterial and Fungal Draft Map
Standard Analysis Data quality control Genome component analysis: gene structure prediction, repetitive sequences, non-coding RNAs |
Bacteria Complete Map Standard Analysis Data quality control Genome component analysis Repeat annotation Coding gene annotation ncRNA annotation GO annotation, KEGG annotation, COG annotation NR annotation, TCDB annotation Pfam annotation Swiss-Prot annotation Genome cycle graph |
Fungus Fine Map Standard Analysis Data quality control Genome survey Repeat annotation Coding gene annotation ncRNA annotation GO annotation, KEGG annotation, NR annotation, KOG annotation Pfam annotation Swiss-Prot annotation. |
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Project Workflow
The first step of the project workflow involves the sample quality control (Sample QC) to ensure that your samples meet the criteria of the Microbial De novo Sequencing. Then, the appropriate library is prepared according to your target organism and application and subsequently tested for its quality (Library QC). Next, the sequenced sample and the resulting data are also checked for their quality (Data QC). Finally, bioinformatic analyses are performed and publication-ready results are provided. The following flowsheet describes the step-by-step protocol our Microbial De novo Sequencing follows.
