Shotgun Metagenomic Sequencing

Comprehensive sequencing of microbial community genomes to characterize taxonomic composition, functional potential, and microbial diversity across complex samples.

Shotgun metagenomic sequencing, including short and long read approaches, analyzes the total genomic DNA in a sample without the need for microbial isolation, cultivation, or target region amplification. This method is essential for studying the 99% of microorganisms that cannot be cultured in laboratories. Unlike targeted methods such as 16S, 18S, or ITS amplicon sequencing, it uses next generation (NGS) and third generation sequencing (TGS) technologies to provide detailed taxonomic annotations, functional profiling, gene prediction, and insights into microbial interactions.

Novogene’s advanced expertise and bioinformatics pipelines deliver high quality data, publication ready results, and tailored analyses, supporting research on microbial community structure, species classification, gene function, and metabolic networks.

Why Choose Novogene for Shotgun Metagenomic Sequencing?

Comprehensive Sequencing in One Run

Profile multiple microorganisms at once without isolation or target amplification for clear, reliable insights.

Advanced Analysis with Proven Expertise

Obtain high‑quality results from diverse sample types, enhanced by long‑read assembly for complete genome mapping.

Localized Support

Regional technical teams provide tailored assistance to support your project needs.

Customizable Solutions

Expert‑designed workflows handle complex samples and challenging research questions with precision.

Fast Turnaround

Receive high‑quality data in as little as two weeks after sample submission.

Top-Quality Data

Industry‑leading sequencing quality backed by Zymo‑validated standards and strict contamination controls.

Applications of Shotgun Metagenomic Sequencing

From taxonomic profiling to functional analysis and metabolic networks, shotgun metagenomic sequencing can be used in many different research topics, including:

Microbiome Profiling Expert

Fully annotates microbial composition and function, revealing the blueprint of life within samples.

Targeted Microbial Radar

Accurately detects key microorganisms related to human health, environmental recovery, and energy synthesis.

Drug Discovery Probe

Deeply investigates the genetic makeup and metabolic mechanisms of microbes, providing foundational clues for drug development.

Interaction Decoder

Delves into microbe-host relationships, opening new pathways for novel drug discovery.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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 contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Novogene provides high-quality products and expert services throughout the entire project workflow. Every step is carefully designed and executed to meet rigorous scientific standards, ensuring exceptional research outcomes. To guarantee the accuracy and reliability of sequencing data, stringent quality control (QC) measures are implemented at each stage of the process. The workflow encompasses key steps such as sample preparation and quantification, fragmentation and library preparation, library quality control, sequencing, and bioinformatics analysis.

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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 contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Resources

Demo Results

1/1

Krona Visualization

Interactive zoomable charts display taxonomic abundance across levels, making complex microbiomes easy to explore.

1/1

Metabolic Pathway

Nodes reflect chemicals and rectangles are enzymes; colors show gene count levels, with red indicating higher values.

1/1

Antibiotic‑Resistant Gene Annotation

Relative abundance of resistance genes is calculated, showing their distribution and resistance types per sample.

1/1

Pfam Cluster Analysis

Bray‑Curtis distance groups samples by protein family profiles, showing both clustering trees and abundance patterns.

1/1

MetaCyc MetaGenomeSeq

Non‑parametric tests detect significantly different features; * marks q<0.05 and ** marks q<0.01 across samples.

1/1

Kraken2 Taxonomic Abundance Heatmap

Shows top 35 taxa with Z‑score normalization; colors indicate abundance levels, with clustering for sample similarity.

Brochure

Metagenomic Solutions Brochure

More Services

Metatranscriptome Sequencing

Amplicon Sequencing

Untargeted Metabolomics

Ready to Start Your Project?

Our platform offers tailored solutions for

your unique experimental needs, ensuring a seamless experience from project design to data delivery.

Shotgun Metagenomic Sequencing

Comprehensive sequencing of microbial community genomes to characterize taxonomic composition, functional potential, and microbial diversity across complex samples.

Why Choose Novogene for Shotgun Metagenomic Sequencing?

Comprehensive Sequencing in One Run

Profile multiple microorganisms at once without isolation or target amplification for clear, reliable insights.

Advanced Analysis with Proven Expertise

Obtain high‑quality results from diverse sample types, enhanced by long‑read assembly for complete genome mapping.

Localized Support

Regional technical teams provide tailored assistance to support your project needs.

Customizable Solutions

Expert‑designed workflows handle complex samples and challenging research questions with precision.

Fast Turnaround

Receive high‑quality data in as little as two weeks after sample submission.

Top-Quality Data

Industry‑leading sequencing quality backed by Zymo‑validated standards and strict contamination controls.

Applications of Shotgun Metagenomic Sequencing

From taxonomic profiling to functional analysis and metabolic networks, shotgun metagenomic sequencing can be used in many different research topics, including:

Microbiome Profiling Expert

Fully annotates microbial composition and function, revealing the blueprint of life within samples.

Targeted Microbial Radar

Accurately detects key microorganisms related to human health, environmental recovery, and energy synthesis.

Drug Discovery Probe

Deeply investigates the genetic makeup and metabolic mechanisms of microbes, providing foundational clues for drug development.

Interaction Decoder

Delves into microbe-host relationships, opening new pathways for novel drug discovery.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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 contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

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)	≥ 5.5 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)	≥ 5.5 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 contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platforms		PacBio Platforms	Nanopore Platforms
Recommended Sequencing Depth	≥ 6Gb for simple environments ≥ 12Gb for complex environments		≥ 10Gb for simple environments	≥ 10Gb for simple environments (Note: Analysis performed using integrated short‑read (NGS) and long‑read sequencing data.)
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.

Project Workflow

Resources

Demo Results

1/1

Krona Visualization

Interactive zoomable charts display taxonomic abundance across levels, making complex microbiomes easy to explore.

1/1

Metabolic Pathway

Nodes reflect chemicals and rectangles are enzymes; colors show gene count levels, with red indicating higher values.

1/1

Antibiotic‑Resistant Gene Annotation

Relative abundance of resistance genes is calculated, showing their distribution and resistance types per sample.

1/1

Pfam Cluster Analysis

Bray‑Curtis distance groups samples by protein family profiles, showing both clustering trees and abundance patterns.

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MetaCyc MetaGenomeSeq

Non‑parametric tests detect significantly different features; * marks q<0.05 and ** marks q<0.01 across samples.

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Kraken2 Taxonomic Abundance Heatmap

Shows top 35 taxa with Z‑score normalization; colors indicate abundance levels, with clustering for sample similarity.

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More Services

Metatranscriptome Sequencing

Amplicon Sequencing

Untargeted Metabolomics

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