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 accurate, complete characterization of any species.
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.
Gel-free and gel-plus methods for preparing mate pair libraries for sequencing from low DNA input.
Speed and simplicity for targeted and small genome sequencing.
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.
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 which provides variant calling, 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 ChicagoTM method on Illumina platforms from multiple DNA inputs.
Highly accurate assembly of long sequencing reads from shorter reads for whole-genome sequencing or genome phasing.NRGene Service
De novo assembly of complex genomes for Ag researchers to deliver long, phased sequences, accurate assembly results on Illumina platforms.
Speed and simplicity for targeted and small genome sequencing.NextSeq Series
Flexible desktop sequencer supporting multiple applications, sequencing 1 Nextera Mate Pair sample per run.HiSeq 2500 System
Power and efficiency for sequencing 4–16 TruSeq Synthetic Long-Read samples or 10–15 Nextera Mate Pair samples per run.HiSeq 3000/4000 Systems
Maximum throughput and lowest cost for production-scale genomics.
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.
De novo assembler suitable for single-cell and isolate genomes.Velvet De Novo Assembly App
De novo assembly of bacterial genomes using the Velvet assembler, with a focus on Nextera Mate Pair data.
Constructs synthetic long reads from shorter sequencing reads for de novo genome assembly and genome finishing.
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.
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.
Shotgun metagenomic sequencing allows researchers to sample all genes in all organisms present in a given complex sample. The method enables microbiologists to evaluate bacterial diversity and study unculturable microorganisms that are otherwise difficult or impossible to analyze. Learn more about shotgun metagenomic sequencing.
De novo sequencing is a first step toward understanding the genetic underpinnings of a plant or animal’s functions and interaction with the environment. 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.
*Data calculations on file. Illumina, Inc., 2015