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Complete Plasmid DNA Sequencing - CD Genomics

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CD Genomics provides complete plasmid DNA sequencing service, and our improved bioinformatics pipelines are available to perform de-novo assembly with no reference required.

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Mitochondrial DNA (mtDNA) sequencing - CD Genomics

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Available on both Illumina and PacBio Platforms, CD Genomics offers mitochondrial DNA sequencing solution you're looking for.

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CD Genomics provides viral genome sequencing service within Illumina and PacBio Platforms. We can create high-quality de novo assembly of large viral genomes and highest possible data quality at low cost.

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Total RNA-Seq provided by CD Genomics offer a comprehensive view of the transcriptome.

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CD Genomics is now providing PacBio Single Molecular Real-Time (SMRT) technology for long-reads sequencing to meet your research goals at a cost-effective way.

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CD Genomics has been providing the accurate and affordable human genome resequencing service for a couple of years. CD Genomics introduces previously hidden PacBio SMRT technology that has great application potential in human genome resequencing. The long single-molecule reads reveal structural variants and produce direct variant phasing information across haplotype blocks and methylation. This is very helpful to broaden the utility of precision medicine efforts to improve human health, and greatly promote the development of human single-gene diseases, complex diseases and tumor genomes.

Application:

1. SV detection
SVs represent genomic rearrangements (typically defined as longer than 50 bp), and SVs may play important roles in human disease, evolution and genetic diversity. Many inherited diseases and cancers have been associated with a large number of SVs in recent years. There has been tremendous progress in the detection of single nucleotide variants (SNVs) in the past quarter century, but intermediate-sized (50 bp to 50 kb) structural variants (SV) remain a challenge with short-read DNA sequencing. The longest read length of the PacBio SMRT sequences is 40~70 K, which can easily cover high repetition and high heterozygosity areas, providing the possibility for SVs detection.

2. Haplotype Genotyping
A haplotype (haploid genotype) is a group of alleles in an organism that is inherited together from a single parent. The correct genotyping of haplotype gene is important; for example, the outcome of unrelated donor marrow transplantation is influenced by donor-recipient matching for HLA. PacBio long reads can span multiple single nucleotides and structural variants, which directly phases the variants into haplotypes.

3. DNA Methylation
DNA methylation is a process by which methyl groups are added to the DNA molecule. It is essential for normal development and is associated with a number of key processes including genomic imprinting, X-chromosome inactivation, repression of transposable elements, aging and carcinogenesis. There are many ways to detect DNA methylation, including whole genome bisulfite sequencing (WGBS), methylated DNA Immunoprecipitation Sequencing (MeDIP) and so on. But these methods are difficult to operate experimentally.

While PacBio platform can describe the direct detection of DNA methylation, without bisulfite conversion according to the difference in the fluorescence pulse signal interval. In addition, the long reads sequencing allows for more thorough regional CpG methylation assessment and increases the capacity for studying the relationship between phased single nucleotide variants and allele-specific CpG methylation.

Key Features and Advantages

Long-reads. It is beneficial for variation information mining of the whole genome, accurate analysis of chromosomal structural variants (SVs) and fusion genes

No PCR amplification. Effectively avoiding the amplification bias, and easily spanning regions with high GC content and high sequence repetition, to ensure the integrity and homogeneity of genome coverage.

Directly detects epigenetic modifications by measuring kinetic variation during base incorporation

Project Workflow

Sample Requirements:

1. DNA amount: ≥ 10 μg
2. DNA Purity: OD260/280 =1.8 ~2.0 without degradation or RNA contamination

Sequencing Strategy: 20 kb Library, ≥ 10X genome coverage depth

Data Analysis

In terms of the extensive experience in human genome resequencing service, CD Genomics provides statistical and bioinformatic data analysis services on SV detection, Haplotype Genotyping, DNA Methylation, and customized bioinformatics services are also available upon request.

Analysis pipeline

CD Genomics provides full whole genome resequencing service package including sample standardization, library construction, deep sequencing, raw data quality control, and bioinformatics analysis. We can tailor this pipeline to your research interest. If you have additional requirements or questions, please feel free to contact us.

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Human Whole Genome PacBio SMRT Sequencing

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CD Genomics has been providing the accurate and affordable human genome resequencing service for a couple of years. CD Genomics introduces previously hidden PacBio SMRT technology that has great application potential in human genome resequencing. The long single-molecule reads reveal structural variants and produce direct variant phasing information across haplotype blocks and methylation.

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CD Genomics provides comprehensive Single-Cell sequencing services to study Single-Cell genomics， which helps to uncover cell lineage relationships.

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CD Genomics proprietary GenSeqTM Technology provides Genomic Data Analysis service. We have extensive experience in helping solve a wide variety of bioinfomatics problems, large and small.

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CD Genomics provides viral genome sequencing service within Illumina and PacBio Platforms. We can create high-quality de novo assembly of large viral genomes and highest possible data quality at low cost.

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Total RNA-Seq provided by CD Genomics offer a comprehensive view of the transcriptome.

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CD Genomics is providing PacBio Single Molecular Real-Time (SMRT) sequencing to increase your research method for bacterial whole genome sequencing. A comprehensive view of the bacterial genome, including genes, regulatory regions, IS elements, phage integration sites, and base modifications is vital to understanding key traits such as antibiotic resistance, virulence, and metabolism.

SMRT Sequencing has long reads (average >15,000 bp, some reads >100,000 bp) and the highest consensus accuracy. It is especially helpful for genome de novo assembly. As we all know,repetitive stretches of DNA are abundant and are one of the main technical challenges that hinder accurate sequencing and genome assembly efforts. In the case of bacteria, the rRNA gene operon is often the largest region of repetitive sequence and range in size between 5 and 7 kb. The Illumina HiSeq platform utilizes sequencing by synthesis technology, that is limited by its read length, currently ranging from 50 to 300 bp, and as it requires PCR amplification of multiple DNA templates before sequencing, there is potential for base-composition bias which may bias the G+C content of the sequences.

The advantage of SMRT long reading, which can overcome the problem of abnormal GC and high duplication of bacterial genomes, often assembled into a single contig. Among all assemblies, the PacBio assembly recovered the highest number of core and virulence proteins, and housekeeping genes based on whole-genome multilocus sequence typing. It is easier to achieve complete assembly or fine map, and help you rapidly advance your research to explore the genetic structure and functions.

Project Workflow

Our highly experienced expert team executes quality management by following every procedure to ensure comprehensive and accurate results. The general workflow for bacterial whole genome sequencing is outlined below.

Sample Amount Recommendation

1. DNA amount: ≥ 5 μg
2. DNA Purity: OD260/280 =1.8 ~2.0 without degradation and RNA contamination

Sequencing Strategy: 20 kb Library, ≥ 60X genome coverage depth

Analysis pipeline

At CD Genomics, we are using the long-read PacBio Sequel platform to support researchers all over the word with bacterial de novo whole genome sequencing needs. Our bioinformatics analysis include: Genome assembly and polishing, gene prediction, genome annotation, and comparative species genomes analysis.
As one of the most famous industry leaders who is skilled in sequencing, CD Genomics not only concentrates on developing cutting-edge technology but also be willing to share our state-of-the-art platforms and sufficient expertise with our clients to promote their brilliant studies. It is our guarantee to provide customers with the best services and finest results at CD Genomics.

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Bacterial Whole Genome de novo Sequencing

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CD Genomics is providing PacBio Single Molecular Real-Time (SMRT) sequencing to increase your research method for bacterial whole genome sequencing. A comprehensive view of the bacterial genome, including genes, regulatory regions, IS elements, phage integration sites, and base modifications is vital to understanding key traits such as antibiotic resistance, virulence, and metabolism.

# data[].attributes.attachment_link.readable_text
CD Genomics has been providing the accurate and affordable human genome resequencing service for a couple of years. CD Genomics introduces previously hidden PacBio SMRT technology that has great application potential in human genome resequencing. The long single-molecule reads reveal structural variants and produce direct variant phasing information across haplotype blocks and methylation. This is very helpful to broaden the utility of precision medicine efforts to improve human health, and greatly promote the development of human single-gene diseases, complex diseases and tumor genomes.

Application:

1. SV detection
SVs represent genomic rearrangements (typically defined as longer than 50 bp), and SVs may play important roles in human disease, evolution and genetic diversity. Many inherited diseases and cancers have been associated with a large number of SVs in recent years. There has been tremendous progress in the detection of single nucleotide variants (SNVs) in the past quarter century, but intermediate-sized (50 bp to 50 kb) structural variants (SV) remain a challenge with short-read DNA sequencing. The longest read length of the PacBio SMRT sequences is 40~70 K, which can easily cover high repetition and high heterozygosity areas, providing the possibility for SVs detection.

2. Haplotype Genotyping
A haplotype (haploid genotype) is a group of alleles in an organism that is inherited together from a single parent. The correct genotyping of haplotype gene is important; for example, the outcome of unrelated donor marrow transplantation is influenced by donor-recipient matching for HLA. PacBio long reads can span multiple single nucleotides and structural variants, which directly phases the variants into haplotypes.

3. DNA Methylation
DNA methylation is a process by which methyl groups are added to the DNA molecule. It is essential for normal development and is associated with a number of key processes including genomic imprinting, X-chromosome inactivation, repression of transposable elements, aging and carcinogenesis. There are many ways to detect DNA methylation, including whole genome bisulfite sequencing (WGBS), methylated DNA Immunoprecipitation Sequencing (MeDIP) and so on. But these methods are difficult to operate experimentally.

While PacBio platform can describe the direct detection of DNA methylation, without bisulfite conversion according to the difference in the fluorescence pulse signal interval. In addition, the long reads sequencing allows for more thorough regional CpG methylation assessment and increases the capacity for studying the relationship between phased single nucleotide variants and allele-specific CpG methylation.

Key Features and Advantages

Long-reads. It is beneficial for variation information mining of the whole genome, accurate analysis of chromosomal structural variants (SVs) and fusion genes

No PCR amplification. Effectively avoiding the amplification bias, and easily spanning regions with high GC content and high sequence repetition, to ensure the integrity and homogeneity of genome coverage.

Directly detects epigenetic modifications by measuring kinetic variation during base incorporation

Project Workflow

Sample Requirements:

1. DNA amount: ≥ 10 μg
2. DNA Purity: OD260/280 =1.8 ~2.0 without degradation or RNA contamination

Sequencing Strategy: 20 kb Library, ≥ 10X genome coverage depth

Data Analysis

In terms of the extensive experience in human genome resequencing service, CD Genomics provides statistical and bioinformatic data analysis services on SV detection, Haplotype Genotyping, DNA Methylation, and customized bioinformatics services are also available upon request.

Analysis pipeline

CD Genomics provides full whole genome resequencing service package including sample standardization, library construction, deep sequencing, raw data quality control, and bioinformatics analysis. We can tailor this pipeline to your research interest. If you have additional requirements or questions, please feel free to contact us.

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Human Whole Genome PacBio SMRT Sequencing

# data[].attributes.attachment_link.description
CD Genomics has been providing the accurate and affordable human genome resequencing service for a couple of years. CD Genomics introduces previously hidden PacBio SMRT technology that has great application potential in human genome resequencing. The long single-molecule reads reveal structural variants and produce direct variant phasing information across haplotype blocks and methylation.

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Single-cell RNA Sequencing - CD Genomics

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CD Genomics provides robust transcriptome research service down to single-cell input levels in high-quality samples These global gene expression patterns in single cells already have dramatically advanced cell biology.

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Genotyping by Sequencing (GBS) - CD Genomics

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CD Genomics is proud to provide genotyping by sequencing service to advance your population based genotyping study in an effective and economic way.

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Get statistical & bioinformatics data analysis services with latest custom-built or open-source software that help explaining large experimental data.

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CD Genomics proprietary GenSeqTM Technology provides Genomic Data Analysis service. We have extensive experience in helping solve a wide variety of bioinfomatics problems, large and small.