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 the entire microbial genome is important for generating accurate reference genomes, for microbial identification, and 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.
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.
Enables efficient purification of intact total nucleic acid, DNA, or RNA from every type of biological material.
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.
Desktop Sequencing SystemsMiSeq System
Speed and simplicity for targeted and small genome sequencing.MiSeq v3 Reagents Kits
Improved chemistry to increase cluster density and read length. Enables up to 15 Gb of output.MiSeq v2 Reagents Kits
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 Series
Flexible desktop sequencer for exome, transcriptome, and whole-genome sequencing.NextSeq 500/550 v2 Kits
Enhanced clustering chemistry yields even higher data quality. Provides 130 or 400 million reads and up to 120 Gb output per run.
High-Throughput Sequencing Systems
Power for high-throughput microbial whole-genome sequencing and flexibility to scale based on your project or workflow needs.
Power and efficiency for large-scale genomics.HiSeq 2500 Reagent Kits
Clustering and sequencing reagents for up to 600 Gb of output.
Maximum throughput, lowest cost for production-scale genomics.HiSeq 3000/4000 SBS Kit and PE Cluster Kit
Leverage patterned flow cell technology to generate up to 1500 Gb (1.5 Tb) of output per dual flow cell run.
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.