Introduction to Small Whole-Genome Sequencing
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.
Small Whole-Genome Sequencing in 3 Simple Steps
See a detailed view of the smallest organisms with this seamless workflow solution.
View Recommended WorkflowAdvantages of Small Genome Sequencing
- Allows investigation of all genes from single organism culture
- Sequences thousands of organisms in parallel
- Provides comprehensive analysis of the microbial or viral genome
- Aids discovery of new biomarkers within a microbial or viral sample by providing distinct gene information from homologous chromosomes, supporting haplotyping
Fast, Culture-Free Microbial Analysis
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.
Recommended Workflow for Small Whole-Genome Sequencing
Library Prep
Nextera DNA Flex Library Prep Kit
A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.
Sequencing
MiSeq Series
Speed and simplicity for targeted and small genome sequencing applications, processing up to 384 small genomes per run.
Data Analysis
BaseSpace Whole-Genome Sequencing App
Push-button extraction of biological data from whole-genome sequences.
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 Small Whole-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 small genome sequencing, from library preparation to data analysis.
Illumina Sequencers Help Characterize and Control Coronavirus
NGS, by rapidly characterizing the full viral genome, plays a critical role in the outbreak of emerging viruses by enabling phylogenetic characterization without a prior knowledge of the potential family. This detailed viral information is enabling public health officials to respond with unprecedented speed and breadth.
Read Article
Whole-Genome Sequencing and Drug Discovery
Learn how Joseph Petrosino, PhD uses whole-genome shotgun sequencing to obtain functional gene pathway and strain-based information in microbiome studies. These methods provide researchers and pharmaceutical companies with data to refine drug discovery and development.
Read ArticleRelated Solutions
Microbial Sequencing
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
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.
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Additional Resources
Tracking the Ebola Virus
Harvard researchers used sequencing to study Ebola outbreaks and understand viral mutations.
Small Genome Sequencing With the NextSeq Series
The NextSeq Series of sequencing systems offers an accessible whole-genome sequencing solution.
Microbiome Studies of Wine and Cheese
Dr. David Mills sequences the microbes involved in wine and cheese production to understand how they influence flavor.
Single-Cell Sequencing of Marine Microbes
Dr. Ramunas Stepanauskas uses single-cell sequencing to characterize bacteria inhabiting the ocean.
Sequencing Tracks a Deadly Porcine Virus
Dr. Ganwu Li and other veterinary scientists use sequencing to study a virus that threatens the pork industry.
Nextera DNA Flex on the iSeq 100 System
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