Novogene
Reliable and high quality NGS data is a key component in genomics research. At Novogene, we use the most effective technology available from world leading providers including Illumina NovaSeq 6000, HiSeq, Oxford Nanopore, Ion Torrent and PacBio Sequel platforms. Over the years our NGS labs have developed optimized NGS processes and protocols to ensure the best possible scientific outcome for your research.
Not only do we offer state of the art NGS technology, we also have the largest sequencing capacity in the world with an annual throughput of over 280,000 human WGS samples.
Sequencing Platform
ILLUMINANovaSeq 6000
Introduced by Illumina in January 2017, the NovaSeq Sequencer provides tremendous scalability and flexibility to accommodate diverse applications and project sizes, for virtually any sequencing method, genome, and scale of project. The NovaSeq sequencer extends applications previously unavailable on HiSeq X Ten, such as expression profiling, whole transcriptome analysis, microbial genome, WES, low pass WGS, etc., while accommodating rapid turnaround, flexible configurations and cost effectiveness. The addition of these NovaSeq sequencers not only expands Novogene¡¯s sequencing capacity, but also greatly reduces our sequencing turnaround time. With the NovaSeq, we are able to sequence up to 48 human whole genomes and produce 6Tb of data per single run as short as 40 hours. System specifications: 850G raw data per lane, 3.4T raw data per Flowcell and 2 x 150 bp read length; 800M raw reads per Flowcell and 2 x 250 bp & 2 x 50 bp reads length;
PACBIO PacBio Sequel II/IIe System
The PacBio Sequel System is the SMRT sequencing platform that provides ultra-long sequencing reads with high consensus accuracy, uniform coverage, and simultaneous epigenetic characterization at single-molecule resolution. The PacBio Sequel System provides 7x more throughput, more scalability, and lower sequencing costs than the PacBio RS II System, while maintaining the same benefits. With the addition of the PacBio Sequel Systems that Novogene acquired in early 2017, Novogene now has the world¡¯s largest SMRT sequencing capacity.
NANOPORE PLATFORM Nanopore PromethION
Oxford Nanopore Technologies offers real-time, long-read, direct and large-scale sequencing of DNA or RNA. Novogene acquired Nanopore PromethION System, the most updated version of Nanopore sequencers with the highest throughput, in 2018. The PromethION system sequences DNA or RNA by Nanopore reader proteins embedded in an electrically resistant membrane. Ultra-long reads span repeat regions in complicated genomes easily, and enhance accuracy of genome assembly and large structure variation detection enormously..
Whole Genome Sequencing
Whole Genome Sequencing is an instrumental technique that is commonly being employed to sequence the entire genomes of animals and plants, respectively, and aims at identifying genomic variations such as SNP, InDel, CNV, and SV. Whole Genome Sequencing is an ideal approach to determine the entirety of genetic information at a single nucleotide level.
Platform Type | Sample Type | Amount (Qubit¢ç) | Purity |
Illumina
NovaSeq 6000 |
Genomic DNA | ¡Ã 200 ng | A260/280=1.8-2.0;
no degradation, |
Genomic DNA
(PCR free non-350bp) |
¡Ã 5 ¥ìg | ||
Genomic DNA
(PCR free -350bp) |
¡Ã 1.2 ¥ìg | ||
PacBio Sequel II DNA CLR library |
HMW Genomic DNA | ¡Ã 8 ¥ìg | A260/280=1.8-2.0; A260/230=1.5-2.6; *NC/QC=0.95-3.00 Fragments should be ¡Ã 40 kb |
PacBio sequel II DNA HiFi library |
HMW Genomic DNA | ¡Ã 15 ¥ìg | A260/280=1.8-2.0; A260/230=1.5-2.6; *NC/QC=0.95-3.00 Fragments should be ¡Ã 30 kb |
Nanopore PromethION | HMW Genomic DNA | ¡Ã 8 ¥ìg | A260/280=1.8-2.0; A260/230=1.5-2.6; Fragments should be ¡Ã 30 kb |
*NC/QC: NanoDrop concetration/Qubit concentration
Platform Type | Illumina NovaSeq 6000 | PacBio Sequel II/IIe | Nanopore PromethION |
Read Length | Paired-end 150 bp | Average > 15 kb | Average > 17 kb |
Recommended
Sequencing Depth |
For SNP/InDel detection: ¡Ã 10¡¿ | For SV detection: ¡Ã 20¡¿ | |
For SV/CNV detection: ¡Ã 20¡¿ | |||
Content of
Analysis |
Standard Analysis
Advanced Analysis
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Standard Analysis
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Whole Exome Sequencing
Whole exome sequencing (WES) employs next-generation sequencing technology (NGS), which provides a cost-efficient alternative to whole genome sequencing (WGS). The human whole exome, composed by about 180,000 exons (protein-coding region of the genome) accounts for only 1-2% of the human genome, but up to 85% of the disease-related mutations associated with Mendelian disorders occur in these regions
Platform Type | Sample Type | Amount (Qubit¢ç) | Purity |
Illumina NovaSeq 6000 | Genomic DNA | ¡Ã 300 ng | A260/280 = 1.8-2.0; no degradation,no contamination |
cfDNA/ctDNA | ¡Ã 30 ng | Fragments should be in multiples of 170 bp, with no genomic contamination |
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Genomic DNA from FFPE tissue | ¡Ã 500 ng | Fragments should be ¡Ã 1000 bp |
Note: Values of sample amount are only listed for your reference. Download the Service Specifications and Sample Requirements to learn more. For detailed information, please contact us with your customized requests.
Sequencing Platform | Illumina NovaSeq 6000 | |||
Read Length | Paired-end 150 bp | |||
Sequencing Depth
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For Mendelian disorder/rare disease: effective sequencing depth above 50¡¿ (6G) | |||
For tumor sample: effective sequencing depth above 100¡¿ (12G) | ||||
Data Analysis |
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mRNA Sequencing (mRNA-seq)
RNA sequencing (RNA-seq) has been transforming the study of cellular functionality, which provides researchers with an unprecedented insight into the transcriptional landscape of cells. Employing the high-throughput and accurate next-generation sequencing technique (NGS), RNA-seq reveals gene expression profiles and describes the continuous variations in the transcriptome. In the RNA-seq technique, the single-stranded messenger RNAs (mRNAs) are selectively captured or enriched, and converted to complementary DNA (cDNA) for library preparation.
Library Type | Sample Type | Amount | RNA Integrity Number (Agilent 2100) | Purity (NanoDrop) |
Eukaryotic RNA-Seq (cDNA library) | Total RNA | 10 Kb for Sequel Inaverage > 15 Kb for Sequel II"}">¡Ã 200 ng | ¡Ã 4.0, with smooth base line | A260/280 = 1.8-2.2 A260/230 ¡Ã 1.8 |
Total RNA (Blood) | ¡Ã 400 ng | ¡Ã 5.8, with smooth base line | ||
Amplified cDNA (double-stranded) | ¡Ã 100 ng | Fragments between 400bp and 5000bp with main peak at ~2000bp | A260/280 = 1.8-2.0 A260/230 ¡Ã 1.8 |
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Eukaryotic RNA-Seq (strand specific library) | Total RNA | ¡Ã 400 ng | ¡Ã 5.8, with smooth base line | A260/280 = 1.8-2.2 A260/230 ¡Ã 1.8 |
Note: Sample amounts are listed for reference only. Download the Service Specifications or Sample Requirements to learn more. For detailed information, please contact us with your customized requests.
Sequencing Platform | Illumina NovaSeq 6000 Sequencing System |
Read Length | Paired-end 150 bp |
Data Output |
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Data Analysis Capability |
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Non-coding RNA Sequencing
lncRNA Sequencing
Long non-Long non-coding RNAs (lncRNAs) are a moderately abundant fraction of the eukaryotic transcriptome, which are comprised of longer than 200nt non-coding RNAs (ncRNAs) , including lincRNAs (intergenic lncRNAs), intronic, anti-sense, sense and bidirectional lncRNAs, which do not encode proteins. Effects of lncRNAs show evidence on multiple cellular functions and perform as prime targets on the regulation of gene transcription, post-transcriptional modifications, and epigenetics. lncRNA sequencing (lncRNA-seq) is a powerful NGS tool to study functional roles in diverse biological processes and human diseases, such as cancer and neurological disorders.
Small RNA Sequencing
Small RNAs (sRNAs) are short RNA molecules, usually non-coding, involved with gene silencing and the post-transcriptional regulation of gene expression. sRNA Sequencing (sRNA-seq) is a method that enables the in-depth investigation of these RNAs, in special microRNAs (miRNAs, 18-40nt in length).
Circular RNA Sequencing
Circular RNA (circRNA) is a highly stable molecule of ncRNA, in form of a covalently closed loop that lacks the 5¡¯end caps and the 3¡¯ poly(A) tails. The circular structure grants to circRNAs resistance against exonuclease digestion, a characteristic that can be exploited in library construction.
Whole Genome Bisulfite Sequencing
DNA methylation at the C5 position of cytosine plays a crucial role in gene expression and chromatin remodeling. Perturbations in methylation patterns are associated with tumorigenesis, neurodegenerative diseases and neurological disorders. Bioinformatic analysis of methylome is widely used in various research areas, including studies on gene regulation, cell differentiation, embryogenesis, aging, occurrence and development of disease, phenotypic diversity and evolution in plants and animals.
Sample Type | Required Amount | Purity |
Genomic DNA | ¡Ã 200 ng | A260/280=1.8-2.0 |
Note: Sample amounts are listed for reference only. Download the Service Specifications or Sample Requirements to learn more. For detailed information, please contact us with your customized requests.
Platform Type | Illumina NovaSeq 6000 |
Read Length | Paired-end 150 bp |
Sequencing Depth | ¡Ã 30¡¿ coverage for the species with reference genome |
Standard Data Analysis |
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Chromatin Immunoprecipitation Sequencing (ChIP-seq)
Chromatin Immunoprecipitation Sequencing (ChIP-seq) provides genome-wide profiling of DNA targets for histone modification, transcription factors, and other DNA-associated proteins. It combines the selectivity of chromatin immuno-precipitation (ChIP) to recover specific protein-DNA complexes, with the power of next-generation sequencing (NGS) to achieve high-throughput sequencing of the recovered DNA.
Sample Type | Required Amount | Fragment size | Purity |
Enriched DNA Sample | ¡Ã 20 ng (Concentration ¡Ã 2 ng/¥ìL) | 100 bp~500 bp | A260/280=1.8-2.0 |
Note: Sample amounts are listed for reference only. Download the Service Specifications or Sample Requirements to learn more. For detailed information, please contact us with your customized requests.
Platform | Illumina NovaSeq 6000 |
Read Length | Pair-end 150 bp |
Sequencing Depth | ¡Ã 20 million read pairs per sample for the species with reference genome |
Standard Data Analysis |
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Reduced Representation Bisulfite Sequencing (RRBS)
Reduced Representation Bisulfite Sequencing (RRBS) detects millions of novel CpG sites based on the improved bisulfite sequencing method, providing coverage to approximately all gene promoters, CpG islands, gene bodies, repetitive DNA sequences, and regulatory elements. It is an NGS-based sequencing platform and combines bisulfite sequencing and restriction enzymes to analyze the genome regions containing high CpG content. This combination allows reduced representation bisulfite sequencing to enhance the efficacy of the sample utilization and provides a perfect platform for clinical applications and pilot research.
Sample Type | Required amount | Purity |
Genomic DNA | ¡Ã 1 ¥ìg | A260/280=1.8-2.0 |
Sequencing Platform | Illumina NovaSeq 6000 Sequencing System |
Read Length | Paired-end 150 bp |
Recommended Data Amount | ¡Ã 10 Gb clean data per sample |
Content of Data Analysis |
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RNA Immunoprecipitation Sequencing (RIP-seq)
RNA immunoprecipitation sequencing (RIP-seq) is a high-throughput RNA sequencing method widely used to study Protein-RNA interactions to detect RNA interactions with the target proteins. The coupling of RIP-seq with other sequencing technologies enables the detection of a large number of RNA-protein complexes in a single run. RIP-seq provides deep insights not only into the central dogma (i.e., transcription and translation) but also in recent research areas like gene regulation by ncRNAs and RNA interference.
Sample Type | Required Amount | Peaks Distribution | Purity |
Enriched RNA Sample | ¡Ã 100 ng (Concentration ¡Ã 3 ng/¥ìL) |
For unfragmented sample, fragment should be ¡Ã 1000 bp. |
A260/280>2.0 |
Sequencing Platform | Illumina NovaSeq 6000 Sequencing System |
Read Length | Paired-end 150bp |
Recommended Data Amount | ¡Ã 20 million read pairs per sample for the species with a reference genome |
Content of Data Analysis |
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16S/18S/ITS Amplicon Metagenomic Sequencing
16S/18S/ITS Amplicon Metagenomic Sequencing is an ultra-deep DNA sequencing method that focuses on sequencing specific target regions (amplicons). Short (<500bp) hypervariable regions of conserved genes or intergenic regions are amplified by PCR and analyzed by next generation sequencing (NGS) technology, to identify and differentiate multiple microbial species from complicated samples. Amplicon metagenomic sequencing is designated to sequence the target genes of 16S ribosomal RNA (rRNA), or 18S rRNA and Internal Transcribed Spacer (ITS) rRNA by universal primers, to describe and compare the phylogeny and taxonomy of bacteria (and archaea) and fungi (such as yeasts, moulds and etc.), respectively.
Types | Amplified Region | Fragment Length | Primers | Sequences (5¡¯- 3¡¯) |
Bacterial 16S | V4 | 300 bp | 515F | GTGCCAGCMGCCGCGGTAA |
806R | GGACTACHVGGGTWTCTAAT | |||
V3-V4 | 470 bp | 341F | CCTAYGGGRBGCASCAG | |
806R | GGACTACNNGGGTATCTAAT | |||
V4-V5 | 450 bp | 515F | GTGCCAGCMGCCGCGGTAA | |
907R | CCGTCAATTCCTTTGAGTTT | |||
V5-V7 (for endophytic) | 435 bp | 799F | AACMGGATTAGATACCCKG | |
1193R | ACGTCATCCCCACCTTCC | |||
Archaeal 16S | V4-V5 | 400-500 bp | Arch519F | CAGCCGCCGCGGTAA |
Arch915R | GTGCTCCCCCGCCAATTCCT |
Types | Amplified Region | Fragment Length | Primers | Sequences (5¡¯- 3¡¯) |
Fungal 18S | V4 | 350 bp | 528F | GCGGTAATTCCAGCTCCAA |
706R | AATCCRAGAATTTCACCTCT | |||
Fungal ITS | ITS1 | 200-400 bp | ITS5-1737F | GGAAGTAAAAGTCGTAACAAGG |
ITS2-2043R | GCTGCGTTCTTCATCGATGC | |||
ITS2 | 380 bp | ITS3-2024F | GCATCGATGAAGAACGCAGC | |
ITS4-2409R | TCCTCCGCTTATTGATATGC | |||
ITS1-1F (for endophytic) | 200-400 bp | ITS1-1F-F | CTTGGTCATTTAGAGGAAGTAA | |
ITS1-1F-R | GCTGCGTTCTTCATCGATGC |
Sample Type | Amount | Volume | Concentration | Purity |
Genomic DNA | ¡Ã 200 ng | ¡Ã 20 ¥ìL | ¡Ã 10 ng/¥ìL | A260/280 = 1.8-2.0 |
Sequencing Platform | Illumina NovaSeq 6000 |
Read Length | Paired-end 250 bp |
Data Output | 30K/50K/100K raw tags |
Standard Data Analysis |
Species annotation |
Shotgun Metagenomic Sequencing
Shotgun metagenomic sequencing provides information on the total genomic DNA from all organisms in a sample, avoiding the need for isolation and cultivation of microorganisms or amplification of target regions. This is crucial because it is believed that nearly 99% of all microorganisms cannot be cultivated in the laboratory. Differently from the targeted approach used in the 16S/18S/ITS amplicon sequencing, shotgun metagenomic sequencing uses next-generation sequencing (NGS) technology to provide not only information on the taxonomic annotations of each organism but also the functional profiling, gene prediction and microbial interaction of the whole community.
Sample Type | Amount | Volume | Concentration | Purity |
Genomic DNA | ¡Ã 200 ng | ¡Ã20 ¥ìL | ¡Ã 10 ng/¥ìL | A260/280 = 1.8-2.0 |
Note: Sample amounts displayed are for reference only. Download the Service Specifications or Sample Requirements to learn more. For detailed information, please contact us with your customized requests.
Sequencing Platform | Illumina NovaSeq 6000 |
Read Length | Pair-end 150 bp |
Recommended Sequencing Depth | ¡Ã 40 million read pairs per sample for species with reference genome |
Standard Data Analysis |
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