Microbial Whole Genome Sequencing

Comprehensive whole-genome sequencing of microorganisms to characterize genetic variation, genome structure, and functional potential.

Microbial whole genome sequencing provides genome-wide information for microorganisms, including bacteria, fungi, viruses and other microbes. It supports microbial identification, strain comparison, comparative genomics and the analysis of genetic variation, genome structure and functional potential.

Novogene Europe supports microbial WGS projects with high-throughput sequencing, quality control and bioinformatics workflows, helping researchers generate reliable data for applications across microbiology, epidemiology, agriculture, ecology and industrial research.

Service Highlights

Diverse Microbial Coverage

Support microbial WGS projects across bacteria, fungi, viruses and other microbes, including pathogenic, probiotic, environmental and industrial strains.

Strain-level Comparison

Whole-genome data supports isolate comparison, lineage analysis and detection of genomic differences across closely related microbial strains.

Scalable Project Support

Support microbial WGS projects from individual strains to larger isolate sets, enabling consistent comparison across samples, sources, conditions or study groups.

Functional Genome Insight

Bioinformatics analysis can support functional annotation and pathway-level interpretation, helping researchers explore microbial traits, adaptation and biological potential.

Applications

Microbial Identification

Microbial WGS supports species and strain characterisation, helping researchers investigate microbial identity, genomic features and relationships between closely related organisms.

AMR and Virulence Research

Microbial WGS can support research into antimicrobial resistance genes, virulence-associated factors and other genomic features linked to microbial behaviour.

Strain Relatedness and Source Tracking

Whole-genome data can help compare microbial strains across samples, sources, locations or time points to investigate relatedness and transmission patterns.

Applied Microbiology

Microbial WGS supports studies across environmental, agricultural, industrial and probiotic microbiology by helping characterise strains and their functional potential.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount (Qubit)	Volume	Concentration	Purity (NanoDropTM/ Agarose Gel)
Microbial whole genome library	Genomic DNA	≥100 ng	≥20 μL	≥5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp
Microbial whole genome library (PCR-free)	Genomic DNA	≥1.2 μg	≥20 μL	≥20 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount (Qubit)	Volume	Concentration	Purity (NanoDropTM/ Agarose Gel)
Microbial whole genome library	Genomic DNA	≥100 ng	≥20 μL	≥5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp
Microbial whole genome library (PCR-free)	Genomic DNA	≥1.2 μg	≥20 μL	≥20 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount (Qubit)	Volume	Concentration	Purity (NanoDropTM/ Agarose Gel)
Microbial whole genome library	Genomic DNA	≥100 ng	≥20 μL	≥5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp
Microbial whole genome library (PCR-free)	Genomic DNA	≥1.2 μg	≥20 μL	≥20 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount (Qubit)	Volume	Concentration	Purity (NanoDropTM/ Agarose Gel)
Microbial whole genome library	Genomic DNA	≥100 ng	≥20 μL	≥5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp
Microbial whole genome library (PCR-free)	Genomic DNA	≥1.2 μg	≥20 μL	≥20 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Platform Type	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Recommended Sequencing Depth	≥ 100x for bacterial genomes
Recommended Sequencing Depth	≥ 50x for fungal genomes
Standard Data Analysis	Data quality control: filtering reads containing adapter or with low quality Alignment with the reference genome, statistics of sequencing depth and coverage SNP/InDel calling, annotation and statistics CNV calling, annotation and statistics SV calling, annotation and statistics

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Platform Type	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Recommended Sequencing Depth	≥ 100x for bacterial genomes
Recommended Sequencing Depth	≥ 50x for fungal genomes
Standard Data Analysis	Data quality control: filtering reads containing adapter or with low quality Alignment with the reference genome, statistics of sequencing depth and coverage SNP/InDel calling, annotation and statistics CNV calling, annotation and statistics SV calling, annotation and statistics

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Platform Type	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Recommended Sequencing Depth	≥ 100x for bacterial genomes
Recommended Sequencing Depth	≥ 50x for fungal genomes
Standard Data Analysis	Data quality control: filtering reads containing adapter or with low quality Alignment with the reference genome, statistics of sequencing depth and coverage SNP/InDel calling, annotation and statistics CNV calling, annotation and statistics SV calling, annotation and statistics

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Platform Type	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Recommended Sequencing Depth	≥ 100x for bacterial genomes
Recommended Sequencing Depth	≥ 50x for fungal genomes
Standard Data Analysis	Data quality control: filtering reads containing adapter or with low quality Alignment with the reference genome, statistics of sequencing depth and coverage SNP/InDel calling, annotation and statistics CNV calling, annotation and statistics SV calling, annotation and statistics

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount (Qubit)	Volume	Concentration	Purity (NanoDropTM/ Agarose Gel)
Microbial whole genome library	Genomic DNA	≥100 ng	≥20 μL	≥5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp
Microbial whole genome library (PCR-free)	Genomic DNA	≥1.2 μg	≥20 μL	≥20 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount (Qubit)	Volume	Concentration	Purity (NanoDropTM/ Agarose Gel)
Microbial whole genome library	Genomic DNA	≥100 ng	≥20 μL	≥5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp
Microbial whole genome library (PCR-free)	Genomic DNA	≥1.2 μg	≥20 μL	≥20 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount (Qubit)	Volume	Concentration	Purity (NanoDropTM/ Agarose Gel)
Microbial whole genome library	Genomic DNA	≥100 ng	≥20 μL	≥5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp
Microbial whole genome library (PCR-free)	Genomic DNA	≥1.2 μg	≥20 μL	≥20 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount (Qubit)	Volume	Concentration	Purity (NanoDropTM/ Agarose Gel)
Microbial whole genome library	Genomic DNA	≥100 ng	≥20 μL	≥5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp
Microbial whole genome library (PCR-free)	Genomic DNA	≥1.2 μg	≥20 μL	≥20 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination Fragments longer than 1000 bp

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Platform Type	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Recommended Sequencing Depth	≥ 100x for bacterial genomes
Recommended Sequencing Depth	≥ 50x for fungal genomes
Standard Data Analysis	Data quality control: filtering reads containing adapter or with low quality Alignment with the reference genome, statistics of sequencing depth and coverage SNP/InDel calling, annotation and statistics CNV calling, annotation and statistics SV calling, annotation and statistics

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Platform Type	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Recommended Sequencing Depth	≥ 100x for bacterial genomes
Recommended Sequencing Depth	≥ 50x for fungal genomes
Standard Data Analysis	Data quality control: filtering reads containing adapter or with low quality Alignment with the reference genome, statistics of sequencing depth and coverage SNP/InDel calling, annotation and statistics CNV calling, annotation and statistics SV calling, annotation and statistics

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Platform Type	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Recommended Sequencing Depth	≥ 100x for bacterial genomes
Recommended Sequencing Depth	≥ 50x for fungal genomes
Standard Data Analysis	Data quality control: filtering reads containing adapter or with low quality Alignment with the reference genome, statistics of sequencing depth and coverage SNP/InDel calling, annotation and statistics CNV calling, annotation and statistics SV calling, annotation and statistics

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Platform Type	Illumina NovaSeq X Plus
Read Length	Paired-end 150 bp
Recommended Sequencing Depth	≥ 100x for bacterial genomes
Recommended Sequencing Depth	≥ 50x for fungal genomes
Standard Data Analysis	Data quality control: filtering reads containing adapter or with low quality Alignment with the reference genome, statistics of sequencing depth and coverage SNP/InDel calling, annotation and statistics CNV calling, annotation and statistics SV calling, annotation and statistics

Resources

Example Analysis Output

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Mutation Spectrum

Compare mutation type proportions across samples to review overall sequence variation patterns.

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COG Functional Classification

Summarise predicted gene functions by COG category to support functional genome interpretation.

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Coding Variant Effects

Summarise coding-region variant effects, including synonymous, non-synonymous and stop-gain or stop-loss changes.

Webinars

Exploring the Microbial World: A Journey through Sequencing Applications

Explore the latest microbial sequencing approaches, including microbial whole genome sequencing, metagenomics, and metatranscriptomics, and learn how advances such as long-read sequencing are expanding our understanding of microbial communities and ecosystems.

Learn More

Explore Genomics Insights

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.

Speak with a Specialist

Have a project in mind?

Send us your enquiry and a Novogene Europe specialist will be in touch.