Small Whole-Genome Sequencing

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.

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Advantages 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 whole-genome sequencing (WGS) 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.

The Time is Now for Microbiome Studies

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.

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COVID-19 Solutions

Illumina NGS is uniquely positioned in an infectious disease surveillance and outbreak model. Compare NGS methods and find solutions to detect and characterize SARS-CoV2, track transmission routes, study co-infection, and investigate viral evolution.

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COVID-19 Solutions

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.

Shortening the Rare Disease Journey

Shortening the Rare Disease Journey

Whole genome sequencing may be the key to helping parents avoid months or years of inconclusive tests. Listen to experts from the Undiagnosed Diseases Network to learn more.

Listen to the Podcast

Related Solutions

Microbial WGS

Sequence and assemble genomes of novel organisms, finish genomes of known organisms, or compare genomes across multiple samples. Learn more about microbial whole-genome sequencing.

Shotgun Metagenomics

Comprehensively analyze all genes in all organisms present in a given complex sample. 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



NextSeq シリーズによる小さいゲノムサイズ生物種のシーケンス
NextSeq シリーズによる小さいゲノムサイズ生物種のシーケンス



Dr. David Millsはワインおよびチーズ製造に関与する微生物のシーケンスにより、これらが製品の風味に及ぼす影響を解明しています。


Dr. Ramunas Stepanauskasは、シングルセルシーケンスを利用して海洋微生物の特性解析を行っています。


Dr. Ganwu Liなどの獣医学研究者は、シーケンスを利用して養豚業に脅威をもたらすウイルスを研究しています。

Nextera DNA Flex on the iSeq 100 System
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