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.
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.
This next-generation sequencing workflow is designed for beginners and describes the recommended methods and products for each step of this application. It includes the Nextera DNA Flex Library Prep Kit, the MiSeq System, and the SRST2 BaseSpace App.View Workflow
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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.Access 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.
A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.Nextera Mate Pair Library Prep Kit
A gel-free method for preparing up to 12 kb mate pair libraries with a low DNA input requirement. It is an ideal approach for de novo sequencing, genome finishing, and the detection of structural variation.Nextera XT Library Prep Kit
Prepare sequencing-ready libraries for small genomes (bacteria, archaea, viruses), amplicons, and plasmids in less than 90 minutes.
Simple, all-inclusive library preparation with shortened gel-free workflows, the ability to sequence the most challenging regions, and the power to identify the greatest number of variants for whole-genome sequencing applications.
Benchtop SequencingiSeq 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 550 System
Flexible desktop sequencer for exome, transcriptome, and whole-genome sequencing.
Power for high-throughput microbial whole-genome sequencing and flexibility to scale based on your project or workflow needs.
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 scaffoldsVelvet 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.
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.Rescaf
Improves scaffolding in bacterial de novo assemblies by removing assembly errors and closing gaps in the consensus sequence.