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.
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.
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 Kit
Fast 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.
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.
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.
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.
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Nat Rev Genet 17 441-582016View Summary
*Data calculations on file. Illumina, Inc., 2015