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.
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 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.
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.
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.BaseSpace Velvet De Novo Assembly App
De novo assembly of bacterial genomes using the Velvet assembler, with a focus on Nextera Mate Pair data.
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.
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.
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.
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.
*Data calculations on file. Illumina, Inc., 2015