Assembling novel genomes

NGS technology for fast, accurate characterization of any species

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.

View Recommended Workflow  

  • 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
Advantages of de novo sequencing

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.

Accurate Genome Assembly
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
Sequencing Method Explorer

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 Kit

Whole genome prep that provides variant calling and phasing for sequencing on Illumina platforms from low DNA input.

Dovetail Service

De 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 Service

De 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 System

Flexible desktop sequencer supporting multiple applications, sequencing 1 Nextera Mate Pair sample per run.

HiSeq 4000 System

High 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 Tool

Compare sequencing platforms and identify the best system for your lab and applications.

Sequencing Reagents

Find kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.

Nextera Mate Pair
BaseSpace SPAdes Genome Assembler App

De novo assembler suitable for single-cell and isolate genomes.

BaseSpace Velvet De Novo Assembly App

De novo assembly of bacterial genomes using the Velvet assembler, with a focus on Nextera Mate Pair data.

Visualization
Integrative Genomics Viewer

Displays alignments and variants from multiple samples for performing complex variant analysis.

BaseSpace Sequence Hub

The 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
The NovaSeq S4 Flow Cell is Here
Microbial Sequencing
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.

Tumor-Normal Sequencing
Tumor-Normal Sequencing

Comparing whole-genome sequencing data from tumor and matched normal samples can provide researchers with valuable insights into cancer mechanisms. Learn more about tumor-normal sequencing.

Metagenomic Sequencing
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
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.

Interested in receiving newsletters, case studies, and information on genomic analysis techniques? Enter your email address.
Sequencing to Improve Food Security
Sequencing to Improve Food Security

Scientists at the Agricultural Research Council in South Africa use sequencing to identify known and novel sweet potato viruses.

Access PDF

Assembling the Kiwi Genome
Assembling the Kiwi Genome

Dr. Diana Le Duc uses mate pair sequencing to understand the evolution of the kiwi bird.

Access PDF
De Novo Bacterial Sequencing on the MiSeq System
De Novo Bacterial Sequencing on the MiSeq System

The MiSeq System is an ideal platform for microbial genome sequencing and de novo assembly.

Access PDF
De Novo Assembly of Bacterial Genomes
De Novo Assembly of Bacterial Genomes

Mate pair technology generates high-quality genome assemblies from multiple microbial species simultaneously.

Access PDF
Accurate Long-Read Sequencing
Accurate Long-Read Sequencing

Illumina technology assembles synthetic long reads from shorter reads to provide more information while maintaining accuracy.

Learn More
Mate Pair Sequencing Technology
Mate Pair Sequencing Technology

Mate pair sequencing uses long-insert, paired-end DNA libraries for de novo genome assembly and genome finishing.

Learn More

*Data calculations on file. Illumina, Inc., 2015