A detailed view of the smallest organisms

Sequencing microbial genomes informs studies in public health, epidemiology, and disease surveillance

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 Workflow  

  • 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

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.

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 small genome sequencing, from library preparation to data analysis.

Click on the below to view products for each workflow step.

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.

Nextera XT DNA Library Prep Kit

Fast and easy library preparation workflow for small genomes, PCR amplicons, and plasmids.

Nextera Mate Pair Library Prep Kit

Gel-free and gel-plus methods for preparing mate pair libraries for sequencing from low DNA input.

iSeq 100 System

Affordable, fast, and accessible sequencing power for targeted or small genome sequencing in any lab.

MiniSeq System

Access cost-effective sequencing, even for low numbers of samples. Sequence up to 50 small genomes per run.

MiSeq System

Speed and simplicity for targeted and small genome sequencing applications, processing up to 384 small genomes per run.

NextSeq 550 System

Flexible desktop sequencer supporting multiple applications, enabling up to 384 small genomes to be sequenced in a single run.

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.

Local Run Manager

An on-premises software solution for creating sequencing runs, monitoring run status, and analyzing data.

BWA Whole-Genome Sequencing App

Processes whole-genome sequencing data using BWA alignment and GATK variant calling.

BaseSpace Whole-Genome Sequencing App

Quickly extracts biological information from whole-genome sequences, using Isaac alignment and variant calling.

SPAdes Genome Assembler

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

BaseSpace Sequence Hub

The Illumina genomics computing environment for NGS data analysis and management.

Can Applying NGS Lead to Better Beer?

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.

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Can Applying NGS Lead to Better Beer?
Microbial Sequencing
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

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.

Recent Publications
Mismatch-repair deficiency predicts response of solid tumors to PD-1 blockade.

Science  2017

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Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.

Cancer Discov 33 1152-82016

View Summary
Computational genomics tools for dissecting tumour-immune cell interactions.

Nat Rev Genet 17 441-582016

View Summary
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Tracking the Ebola Virus
Tracking the Ebola Virus

Harvard researchers used sequencing to study Ebola outbreaks and understand viral mutations.

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Small Genome Sequencing With the NextSeq Series
Small Genome Sequencing With the NextSeq Series

The NextSeq Series of sequencing systems offers an accessible whole-genome sequencing solution.

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Microbiome Studies of Wine and Cheese
Microbiome Studies of Wine and Cheese

Dr. David Mills sequences the microbes involved in wine and cheese production to understand how they influence flavor.

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Single-Cell Sequencing of Marine Microbes
Single-Cell Sequencing of Marine Microbes

Dr. Ramunas Stepanauskas uses single-cell sequencing to characterize bacteria inhabiting the ocean.

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Sequencing Tracks a Deadly Porcine Virus
Sequencing Tracks a Deadly Porcine Virus

Dr. Ganwu Li and other veterinary scientists use sequencing to study a virus that threatens the pork industry.

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