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Small genome sequencing (≤ 5 Mb) involves sequencing the entire genome of a bacterium, virus, or other microbe, and then comparing the sequence to a known reference. Sequencing small microbial genomes can be useful for food testing in public health, infectious disease surveillance, molecular epidemiology studies, and environmental metagenomics.
See a detailed view of the smallest organisms with this seamless workflow solution.
Unlike traditional approaches, small genome sequencing studies using next-generation sequencing (NGS) do not rely on labor-intensive cloning steps. NGS also enables biologists to sequence hundreds of organisms simultaneously via multiplexing. NGS can identify low-frequency variants, genomic rearrangements, and other genetic changes that might be missed or are too costly to identify using other methods. For small genomes, DNA libraries can be prepared, sequenced, and analyzed in as little as 2 days.
A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.
Speed and simplicity for targeted and small genome sequencing applications, processing up to 384 small genomes per run.
Push-button extraction of biological data from whole-genome sequences.
Use this interactive tool to explore experimental next-generation sequencing (NGS) library preparation methods compiled from the scientific literature.
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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 small genome sequencing, from library preparation to data analysis.
Click on the below to view products for each workflow step.
A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.
Nextera XT DNA Library Prep KitFast and easy library preparation workflow for small genomes, PCR amplicons, and plasmids.
Gel-free and gel-plus methods for preparing mate pair libraries for sequencing from low DNA input.
Affordable, fast, and accessible sequencing power for targeted or small genome sequencing in any lab.
MiniSeq SystemAccess cost-effective sequencing, even for low numbers of samples. Sequence up to 50 small genomes per run.
MiSeq SystemSpeed and simplicity for targeted and small genome sequencing applications, processing up to 384 small genomes per run.
Flexible desktop sequencer supporting multiple applications, enabling up to 384 small genomes to be sequenced in a single run.
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.
An on-premises software solution for creating sequencing runs, monitoring run status, and analyzing data.
BWA Whole-Genome Sequencing AppProcesses whole-genome sequencing data using BWA alignment and GATK variant calling.
BaseSpace Whole-Genome Sequencing AppQuickly extracts biological information from whole-genome sequences, using Isaac alignment and variant calling.
De novo assembler suitable for single-cell and isolate genomes.
BaseSpace Sequence HubThe Illumina genomics computing environment for NGS data analysis and management.
An international group of scientists, yeast producers, and brewers sequenced 96 yeast strains to learn how genetics can influence the flavor of beer. Their findings, published in Cell, could help brewers make better beers.
Read Article
Microbial whole-genome sequencing is an important research 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.
Shotgun metagenomics enables comprehensive analysis of all genes in all organisms present in a given complex sample. It enables researchers to detect very low abundance microbes that may be missed or are too expensive to identify using other methods. Learn more about shotgun metagenomic sequencing.
Science 2017
View SummaryCancer Discov 33 1152-82016
View SummaryNat Rev Genet 17 441-582016
View Summary
Harvard researchers used sequencing to study Ebola outbreaks and understand viral mutations.
The NextSeq Series of sequencing systems offers an accessible whole-genome sequencing solution.
Dr. David Mills sequences the microbes involved in wine and cheese production to understand how they influence flavor.
Dr. Ramunas Stepanauskas uses single-cell sequencing to characterize bacteria inhabiting the ocean.
Dr. Ganwu Li and other veterinary scientists use sequencing to study a virus that threatens the pork industry.
View tips on transitioning to Nextera DNA Flex on the iSeq 100 System, including considerations for viral and bacterial sequencing.
*Data calculations on file. Illumina, Inc., 2015