Shotgun Metagenomics Sequencing

DNA-based microbial community profiling to explore taxonomic composition, functional potential and genome-resolved insights

Shotgun metagenomic sequencing analyses total DNA extracted from complex microbial communities, without relying on targeted amplification or microbial culturing. It provides a broader view of community composition and genetic potential, helping researchers investigate which organisms are present and what functional capabilities may be encoded within the microbiome.

Novogene Europe supports shotgun metagenomic sequencing projects with short-read and long-read sequencing options, including Illumina, PacBio and Oxford Nanopore, depending on project goals and sample requirements. Bioinformatics workflows can support taxonomic profiling, metagenome assembly, gene prediction, functional annotation, pathway analysis, antimicrobial resistance gene analysis and genome-resolved approaches such as metagenome-assembled genome analysis where suitable.

Service Highlights

DNA-based Community Profiling

Analyse total microbial DNA to profile community composition and explore the genetic potential encoded within complex microbiome samples.

Short- and Long-read Options

Support shotgun metagenomic projects using Illumina, PacBio or Oxford Nanopore sequencing options, depending on project goals and sample requirements.

Taxonomic and Functional Analysis

Bioinformatics workflows support species annotation, gene prediction, functional annotation and pathway-level interpretation of microbial community data.

Assembly and MAG Analysis

Metagenome assembly and genome-resolved analysis can support recovery of metagenome-assembled genomes where sample complexity and data quality allow.

Applications

Microbiome Composition and Diversity

Shotgun metagenomics helps researchers profile microbial community composition and diversity across environmental, host-associated or experimental samples.

Functional Potential Analysis

DNA-level gene and pathway analysis can support research into microbial metabolic potential, community functions and ecosystem capabilities.

Antimicrobial Resistance and Virulence Research

Shotgun metagenomics can support analysis of antimicrobial resistance genes, virulence-associated factors and other functional markers across microbiome samples.

Genome-resolved Microbiome Research

Metagenome assembly and MAG analysis can help link genes and pathways to microbial community members where data quality and sample complexity allow.

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.

Service	Sample Type	Amount	Volume	Concentration	Purity
Shotgun Metagenomic Sequencing	Total DNA	≥ 100 ng	≥20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0.no degradation, no contamination Fragments longer than 500 bp
Shotgun Metagenomic Sequencing（PacBio）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K
Shotgun Metagenomic Sequencing（Nanopore）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K

HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

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.

Service	Sample Type	Amount	Volume	Concentration	Purity
Shotgun Metagenomic Sequencing	Total DNA	≥ 100 ng	≥20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0.no degradation, no contamination Fragments longer than 500 bp
Shotgun Metagenomic Sequencing（PacBio）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K
Shotgun Metagenomic Sequencing（Nanopore）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K

HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

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.

Service	Sample Type	Amount	Volume	Concentration	Purity
Shotgun Metagenomic Sequencing	Total DNA	≥ 100 ng	≥20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0.no degradation, no contamination Fragments longer than 500 bp
Shotgun Metagenomic Sequencing（PacBio）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K
Shotgun Metagenomic Sequencing（Nanopore）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K

HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

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.

Service	Sample Type	Amount	Volume	Concentration	Purity
Shotgun Metagenomic Sequencing	Total DNA	≥ 100 ng	≥20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0.no degradation, no contamination Fragments longer than 500 bp
Shotgun Metagenomic Sequencing（PacBio）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K
Shotgun Metagenomic Sequencing（Nanopore）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K

HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

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.

Sequencing Platform	Illumina NovaSeq Platform		PacBio Revio Platform	Oxford Nanopore Platform
Sequencing Strategy	Pair-end 150 bp		CCS (Circular Consensus Sequencing) Mode	Single-pass Sequencing
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments(Note:Integrated analysis of second-generation and third-generation sequencing data was performed.)
Analysis Options (Choose among these three)	Standard Analysis(Assembly-based)	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, eggNOG, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses
	MetaPhlAn4-HUMAnN3(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( MetaCyc, KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-
	Kraken2(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-

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.

Sequencing Platform	Illumina NovaSeq Platform		PacBio Revio Platform	Oxford Nanopore Platform
Sequencing Strategy	Pair-end 150 bp		CCS (Circular Consensus Sequencing) Mode	Single-pass Sequencing
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments(Note:Integrated analysis of second-generation and third-generation sequencing data was performed.)
Analysis Options (Choose among these three)	Standard Analysis(Assembly-based)	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, eggNOG, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses
	MetaPhlAn4-HUMAnN3(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( MetaCyc, KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-
	Kraken2(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-

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.

Sequencing Platform	Illumina NovaSeq Platform		PacBio Revio Platform	Oxford Nanopore Platform
Sequencing Strategy	Pair-end 150 bp		CCS (Circular Consensus Sequencing) Mode	Single-pass Sequencing
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments(Note:Integrated analysis of second-generation and third-generation sequencing data was performed.)
Analysis Options (Choose among these three)	Standard Analysis(Assembly-based)	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, eggNOG, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses
	MetaPhlAn4-HUMAnN3(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( MetaCyc, KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-
	Kraken2(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-

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.

Sequencing Platform	Illumina NovaSeq Platform		PacBio Revio Platform	Oxford Nanopore Platform
Sequencing Strategy	Pair-end 150 bp		CCS (Circular Consensus Sequencing) Mode	Single-pass Sequencing
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments(Note:Integrated analysis of second-generation and third-generation sequencing data was performed.)
Analysis Options (Choose among these three)	Standard Analysis(Assembly-based)	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, eggNOG, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses
	MetaPhlAn4-HUMAnN3(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( MetaCyc, KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-
	Kraken2(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-

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.

Service	Sample Type	Amount	Volume	Concentration	Purity
Shotgun Metagenomic Sequencing	Total DNA	≥ 100 ng	≥20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0.no degradation, no contamination Fragments longer than 500 bp
Shotgun Metagenomic Sequencing（PacBio）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K
Shotgun Metagenomic Sequencing（Nanopore）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K

HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

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.

Service	Sample Type	Amount	Volume	Concentration	Purity
Shotgun Metagenomic Sequencing	Total DNA	≥ 100 ng	≥20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0.no degradation, no contamination Fragments longer than 500 bp
Shotgun Metagenomic Sequencing（PacBio）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K
Shotgun Metagenomic Sequencing（Nanopore）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K

HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

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.

Service	Sample Type	Amount	Volume	Concentration	Purity
Shotgun Metagenomic Sequencing	Total DNA	≥ 100 ng	≥20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0.no degradation, no contamination Fragments longer than 500 bp
Shotgun Metagenomic Sequencing（PacBio）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K
Shotgun Metagenomic Sequencing（Nanopore）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K

HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

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.

Service	Sample Type	Amount	Volume	Concentration	Purity
Shotgun Metagenomic Sequencing	Total DNA	≥ 100 ng	≥20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0.no degradation, no contamination Fragments longer than 500 bp
Shotgun Metagenomic Sequencing（PacBio）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K
Shotgun Metagenomic Sequencing（Nanopore）	HMW genomic DNA (metagenomics)	≥5 μg	≥50 μL	≥80 ng/μL	OD260/280=1.7~2.5. OD260/230=1.1~2.6. NC/QC=0.95~4.00 Fragments should be ≥10K

HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

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.

Sequencing Platform	Illumina NovaSeq Platform		PacBio Revio Platform	Oxford Nanopore Platform
Sequencing Strategy	Pair-end 150 bp		CCS (Circular Consensus Sequencing) Mode	Single-pass Sequencing
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments(Note:Integrated analysis of second-generation and third-generation sequencing data was performed.)
Analysis Options (Choose among these three)	Standard Analysis(Assembly-based)	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, eggNOG, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses
	MetaPhlAn4-HUMAnN3(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( MetaCyc, KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-
	Kraken2(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-

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.

Sequencing Platform	Illumina NovaSeq Platform		PacBio Revio Platform	Oxford Nanopore Platform
Sequencing Strategy	Pair-end 150 bp		CCS (Circular Consensus Sequencing) Mode	Single-pass Sequencing
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments(Note:Integrated analysis of second-generation and third-generation sequencing data was performed.)
Analysis Options (Choose among these three)	Standard Analysis(Assembly-based)	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, eggNOG, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses
	MetaPhlAn4-HUMAnN3(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( MetaCyc, KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-
	Kraken2(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-

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.

Sequencing Platform	Illumina NovaSeq Platform		PacBio Revio Platform	Oxford Nanopore Platform
Sequencing Strategy	Pair-end 150 bp		CCS (Circular Consensus Sequencing) Mode	Single-pass Sequencing
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments(Note:Integrated analysis of second-generation and third-generation sequencing data was performed.)
Analysis Options (Choose among these three)	Standard Analysis(Assembly-based)	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, eggNOG, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses
	MetaPhlAn4-HUMAnN3(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( MetaCyc, KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-
	Kraken2(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-

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.

Sequencing Platform	Illumina NovaSeq Platform		PacBio Revio Platform	Oxford Nanopore Platform
Sequencing Strategy	Pair-end 150 bp		CCS (Circular Consensus Sequencing) Mode	Single-pass Sequencing
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments(Note:Integrated analysis of second-generation and third-generation sequencing data was performed.)
Analysis Options (Choose among these three)	Standard Analysis(Assembly-based)	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, eggNOG, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses	Data quality control (host contamination removal if required) Metagenome Assembly Gene Prediction Taxonomy Annotation Function Annotation (KEGG, GO, CAZY…etc) Alpha and Beta Diversity Analyses Antibiotic Resistance Gene and Mobile Genetic Elements Annotation and Analyses
	MetaPhlAn4-HUMAnN3(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( MetaCyc, KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-
	Kraken2(Reads-Mapping Based)	Data quality control (host contamination removal if required) Taxonomy Annotation Function Annotation ( KEGG, eggNOG, GO…etc) Alpha and Beta Diversity Analyses Differential analysis between groups of species and function.	-	-

Resources

Example Analysis Output

1/1

Taxonomic Composition

Summarise microbial community composition across samples using taxonomic abundance profiles.

1/1

ARG Taxonomy Association

Explore relationships between antimicrobial resistance genes and associated microbial taxa.

1/1

Beta Diversity PCoA

Visualise differences in microbial community structure across samples or groups.

1/1

Krona Taxonomy View

Explore interactive taxonomic classification results across microbial community samples.

1/1

Taxa Heatmap

Compare abundance patterns of annotated taxa across samples and experimental groups.

1/1

Mobile Element Overview

Visualise mobile genetic element patterns across samples or annotated genomic regions.

Webinars

Decoding Microbial Communities: Sequencing Solutions for Microbiome Research

Explore the latest approaches for studying microbial communities using amplicon sequencing, metagenomics, and metatranscriptomics. This webinar will highlight how these technologies can reveal microbial diversity, function, and interactions across human, environmental, and industrial ecosystems.

Learn More

Explore Microbiome 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.