What Is De Novo Sequencing?
De novo sequencing refers to sequencing a novel genome where there is no reference sequence available for alignment. Sequence reads are assembled as contigs, and the coverage quality of de novo sequence data depends on the size and continuity of the contigs (ie, the number of gaps in the data).
Next-generation sequencing (NGS) enables faster, more accurate characterization of any species compared to traditional methods, such as Sanger sequencing. Illumina offers mate pair sequencing and long-read technology to complement shorter reads for comprehensive, accurate characterization of any species.
De Novo Sequencing in 3 Steps
Assemble novel bacterial genomes with this simple workflow solution.
Advantages of De Novo Sequencing
- Generates accurate reference sequences, even for complex or polyploid genomes
- Provides useful information for mapping genomes of novel organisms or finishing genomes of known organisms
- Clarifies highly similar or repetitive regions for accurate de novo assembly
- Identifies structural variants and complex rearrangements, such as deletions, inversions, or translocations
Accurate Genome Assembly
When sequencing a genome for the first time, use a combined approach for higher-quality assemblies. Combining short-insert, paired-end and long-insert, mate pair sequences is the ideal way to maximize coverage. The short reads, sequenced at higher depths, can fill in gaps not covered by the long inserts.
This combination enables detection of the widest range of structural variant types and is essential for accurate identification of complex rearrangements. Synthetic long reads can also aid assembly by providing long contigs that are “stitched” together from shorter reads to maintain accuracy.
Recommended Workflow for De Novo Bacterial Sequencing
Library Prep
Nextera Mate Pair Library Prep Kit
Gel-free and gel-plus methods for preparing mate pair libraries for sequencing from low DNA input.
Data Analysis
Velvet De Novo Assembly and Prokka Genome Annotation
Push-button de novo assembly pipeline for bacterial samples, for rapid annotation of genes and identification of coding regions.
Assembly Report
Prokka Input Form
Sequencing Method Explorer
Use this interactive tool to explore experimental next-generation sequencing (NGS) library preparation methods compiled from the scientific literature.
Find a Method
Comprehensive De Novo Genome Sequencing Workflow
Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of global sequencing data.*
In addition to our industry-leading data quality, Illumina offers integrated workflows that simplify de novo sequencing, from library preparation to data analysis.
Click on the below to view products for each workflow step.
Nextera Mate Pair Library Prep Kit
Gel-free and gel-plus methods for preparing mate pair libraries for sequencing from low DNA input.
10x Genomics Chromium Genome Library Prep KitWhole genome prep that provides variant calling and phasing for sequencing on Illumina platforms from low DNA input.
Dovetail ServiceDe novo assembly for a large range of genomes using the proprietary Dovetail Chicago TM method on Illumina platforms from multiple DNA inputs.
Long-Read Sequencing Technology
Highly accurate assembly of DNA fragments into long reads for whole-genome sequencing or genome phasing.
NRGene ServiceDe novo assembly of complex genomes for Ag researchers to deliver long, phased sequences and accurate assembly results on Illumina platforms.
MiSeq System
Speed and simplicity for targeted and small genome sequencing.
NextSeq 550 SystemFlexible desktop sequencer supporting multiple applications, sequencing 1 Nextera Mate Pair sample per run.
HiSeq 4000 SystemHigh throughput and low cost for production-scale genomics.
NovaSeq 6000 System
Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.
Platform Comparison ToolCompare sequencing platforms and identify the best system for your lab and applications.
Sequencing ReagentsFind kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.
Nextera Mate Pair
BaseSpace SPAdes Genome Assembler AppDe novo assembler suitable for single-cell and isolate genomes.
BaseSpace Velvet De Novo Assembly AppDe novo assembly of bacterial genomes using the Velvet assembler, with a focus on Nextera Mate Pair data.
Visualization
Integrative Genomics ViewerDisplays alignments and variants from multiple samples for performing complex variant analysis.
BaseSpace Sequence HubThe Illumina genomics computing environment for NGS data analysis and management.
The NovaSeq S4 Flow Cell is Here
Reagent kits for the NovaSeq 6000 System are now available in three flow cell configurations: S1 is ideal for smaller batch sizes or in situations where rapid turnaround time is required. S2 is a quick, powerful, and cost-effective option for high-throughput applications. S4 offers tunable output and additional flexibility.
View Kits
Related Solutions
Microbial Sequencing
Microbial whole-genome sequencing is an important tool for mapping genomes of novel organisms, finishing genomes of known organisms, or comparing genomes across multiple samples. Learn more about microbial whole-genome sequencing.
Cancer Whole-Genome Sequencing
Whole-genome sequencing of tumor samples provides a comprehensive view of the unique mutations in cancer tissue, informing analysis of oncogenes, tumor suppressors, and other risk factors. Learn more about cancer WGS.
Metagenomic Sequencing
Shotgun metagenomic sequencing enables microbiologists to evaluate bacterial diversity and study unculturable microorganisms that are otherwise difficult or impossible to analyze. Learn more about metagenomic sequencing.
Plant and Animal Sequencing
De novo sequencing can provide insight into a plant or animal’s functions and environmental interactions. Some researchers use the assembled genome to assign map positions and stack diverse breed information for subsequent SNP discovery. Learn more about plant and animal sequencing.
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Additional Resources
Sequencing to Improve Food Security
Scientists at the Agricultural Research Council in South Africa use sequencing to identify known and novel sweet potato viruses.
Assembling the Kiwi Genome
Dr. Diana Le Duc uses de novo sequencing to understand the evolution of the kiwi bird.
De Novo Bacterial Sequencing
The MiSeq System is an ideal platform for microbial genome sequencing and de novo assembly.
De Novo Assembly of Bacterial Genomes
Mate pair technology generates high-quality genome assemblies from multiple microbial species simultaneously.
*Data calculations on file. Illumina, Inc., 2015