Sequence hundreds of organisms with the power of multiplexing

Generate accurate reference genomes and perform comparative genomic studies

Microbial Whole-Genome Sequencing

Microbial whole-genome sequencing is an important tool for mapping genomes of novel organisms, finishing genomes of known organisms, or comparing genomes across multiple samples. Sequencing entire bacterial, viral, and other microbial genomes is important for generating accurate reference genomes, for microbial identification, and for other comparative genomic studies.

Unlike capillary sequencing or PCR-based approaches, next-generation sequencing (NGS) allows microbiology researchers to sequence hundreds of organisms with the power of multiplexing. Unlike traditional methods, NGS-based microbial genome sequencing doesn’t rely on labor-intensive cloning steps, saving time and simplifying the workflow. NGS can identify low-frequency variants and genome rearrangements that may be missed or are too expensive to identify using other methods.

Methods Guide for Microbial Whole-Genome Sequencing
Methods Guide for Microbial Whole-Genome Sequencing

Sequence hundreds of organisms simultaneously, generate accurate reference genomes, and perform comparative genomic studies.

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De novo whole-genome sequencing involves assembling a genome without the use of a genomic reference and is often used to sequence novel microbial genomes. Illumina sequencers provide unparalleled raw read accuracy, read length and read depth for high-quality draft and complete microbial genome assemblies.

Microbial whole-genome resequencing involves sequencing the entire genome of a bacteria, virus, or other microbe, and comparing the sequence to that of a known reference. Generating rapid and accurate microbial genome sequence information is critical for detecting low frequency mutations, finding key deletions and insertions, and discovering other genetic changes among microbial strains.

Featured Microbial Whole-Genome Sequencing Workflow

This next-generation sequencing workflow is designed for beginners and describes the recommended methods and products for each step of this application.

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Featured Microbial Whole-Genome Sequencing Workflow

Featured Microbial Research Stories

Illumina Sequencers Help Characterize and Control Coronavirus
Illumina Sequencers Help Characterize and Control Coronavirus

This detailed viral information is enabling public health officials to respond with unprecedented speed and breadth.

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The Fight Against Ebola
The Fight Against Ebola

In 2014, the world's eyes were pointed toward West Africa, where an Ebola outbreak was claiming the lives of thousands of people. Long before that, the virus was quietly circulating.

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The Power and Portability of the iSeq
The Power and Portability of the iSeq

Local scientists used the iSeq 100 System to analyze transmission patterns and trace the origin of the Ebola outbreak in the Democratic Republic of Congo.

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Microbiology Methods Guide

All the information you need, from library preparation to final data analysis. Select the best tools for a broad range of microbiology applications for your laboratory.

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Microbiology Methods Guide

There are multiple ways to perform these experiments, but these are some suggested products for each step of the workflow.

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

Illumina DNA Prep 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 Library Prep Kit

Prepare sequencing-ready libraries for small genomes (bacteria, archaea, viruses), amplicons, and plasmids in less than 90 minutes.

TruSeq DNA PCR-Free Library Preparation Kits

Simple, all-inclusive library preparation with shortened gel-free workflows, the ability to sequence challenging regions, and the power to identify variants across the genome.

iSeq System

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

MiniSeq System

Supports a broad range of targeted DNA and RNA applications.

MiSeq System

Several kit configurations, including a 500 cycle kit for efficient mapping of small genomes. Micro and nano formats available for cost-efficient sequencing of 1-4 samples.

NextSeq 1000 & 2000 Systems

Groundbreaking benchtop sequencers allow you to explore new discoveries across a variety of current and emerging applications.

NovaSeq 6000 System

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

BaseSpace Apps for de novo assemblies or mapping of contigs and scaffolds

Velvet de novo Assembly

De novo assembly of bacteria using the Velvet assembler with a focus on Nextera Mate Pair data.

String Graph Assembler

Performs a contig assembly, builds scaffolds, removes mate pair adapter sequences, and calculates assembly quality metrics.

SPAdes Genome Assembler

Online bioinformatics tool for assembling microbial genome sequences.

Prokka Genome Annotation

Rapidly annotates genes and identifies coding sequences in prokaryotic genomes, from de novo assembly sequences.


Improves scaffolding in bacterial de novo assemblies by removing assembly errors and closing gaps in the consensus sequence.


Tell-Read and Tell-Link App links reads and creates assemblies for de novo WGS.

Frequently Purchased Together

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De Novo Bacterial Sequencing
De Novo Bacterial Sequencing Overview

Learn how high-quality paired-end reads ensure superior bacterial genome assembly.

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Microbiology: Spotlight on Food Pathogen Testing
Microbiology: Spotlight on Food Pathogen Testing

Overview of Illumina next-generation sequencing platforms and relevant applications and use cases for food pathogen testing.

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Push-Button De Novo Microbial Genome Sequence Assembly
Push-Button De Novo Microbial Genome Sequence Assembly

Explore options for performing de novo assembly of microbial and other genomes.

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Assembly of the Saccharomyces cerevisiae Genome
Assembly of the Saccharomyces cerevisiae Genome

This application note describes a complete workflow for sequencing small genomes with MiSeq.

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NGS for microbial genomes and infection control
NGS for Microbial Genomes and Infection Control

Global collaboration of researchers is using the MiSeq System to understand the evolution and spread of drug-resistant bacteria.

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TELL-Seq: Bringing Speed and Accuracy to Long-Range Sequencing
TELL-Seq: Bringing Speed and Accuracy to Long-Range Sequencing

TELL-Seq technology is a simple library prep solution which enables Illumina NGS systems to generate highly accurate and economical long-range sequencing information.

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