The genome represents the entire genetic information of an organism. The most comprehensive collection of an individual’s genetic information is provided by analyzing the whole genome using next-generation sequencing (NGS) technology. By comparing the individual’s genetic information to a reference genome single nucleotide variants (SNVs), small insertions and deletions (indels), copy number variations (CNVs), and structural variants (SVs) can be studied.
Whole genome sequencing studies contribute to:
- cancer studies, personalized medicine approaches, and translational research
- discovery of biomarkers and understanding of pharmacogenetics
- disease research
- plant and animal breeding programs
- examination of microorganisms
You can choose between various Whole Genome Sequencing products to receive the comprehensive genome analysis you need for your research project.
Our service covers the full project workflow: from expert consulting and comprehensive bioinformatic evaluation to a clear and structured project report. The project report provides insights into sample quality, sequencing parameters, bioinformatic analysis, and results.
CeGaT Is the Best Partner for Sequencing Your Project
Explore Our Product Portfolio for Genome Sequencing
We offer different Whole Genome Sequencing (WGS) products to address a variety of research questions. Our WGS products are either processed on our Illumina sequencing platforms using short-read sequencing or on our PacBio sequencing platforms using long-read sequencing. Would you like to have bioinformatic analyses performed on your data in addition to the included deliverables? Each of our products can be supplemented with further services. We are happy to advise you.
Short-Read WGS
WGS Large Classic | WGS Small Classic | WGS Flex |
Species | Species | Species |
DNA quality | DNA quality | DNA quality |
PCR amplification Yes/No | PCR amplification Yes | PCR amplification Yes/No |
Read length | Read length | Read length |
Sequencing platform | Sequencing platform | Sequencing platform |
Output | Output | Output |
Included deliverables Project report & files in FASTQ format | Included deliverables | Included deliverables |
Long-Read WGS
HiFi WGS Classic | HiFi WGS Premium | HiFi WGS Flex |
Species Human | Species Human | Species Diverse |
DNA quality Human high molecular weight DNA | DNA quality Human high molecular weight DNA | DNA quality High molecular weight DNA |
PCR amplification No | PCR amplification No | PCR amplification No |
Read length On average 15 – 20 kb | Read length On average 15 – 20 kb | Read length On average 15 – 20 kb |
Sequencing platform PacBio | Sequencing platform PacBio | Sequencing platform PacBio |
Output 3–4 million HiFi reads | Output 6–8 million HiFi reads | Output Depending on project |
Included deliverables Project report & files in FASTQ format | Included deliverables | Included deliverables |
Bioinformatics
Raw sequencing data are automatically processed. We offer different levels of bioinformatic analysis. The default level is Level 1. With increasing bioinformatic level, more data are delivered. All higher levels include the data from the lower levels. In addition to the data, and independent of the analysis level, a project report is generated.
Analysis of Our Short-Read WGS Products
- WGS Large Classic
- WGS Small Classic
- WGS Flex
WGS Large Classic and WGS Flex are analyzed with the Illumina DRAGEN Bio-IT Platform. WGS Small Classic is analyzed with the CeGaT pipeline.
For human samples, we can perform the analyses based on the human references hg19 or GRCh38.
Analysis of Our Long-Read WGS Products
- HiFi WGS Classic
- HiFi WGS Premium
- HiFi WGS Flex
Level 3 is only available for human samples with GRCh38 as a reference genome.
Level 1:
- demultiplexing and adapter trimming of the sequencing data (FASTQ format)
- metrices (CSV format)
- MultiQC report (HTML format)
Level 2:
- mapping of the sequencing data (BAM format)
- prediction of ploidy of sex chromosomes (CSV file) (only for human samples)
- metrices (CSV format)
Level 3:
- calling of single nucleotide variants (SNVs) and small insertions and deletions (indels) (VCF format)
- calling of regions of homozygosity (ROH) (BED and CSV format) (only for human samples)
- metrices (CSV format)
Level 4:
- annotation of the SNVs and indels (JSON and TSV format) (only for human samples)
Level 5:
- calling of copy number variations (CNVs) (VCF and GFF3 format) including annotations (JSON and TSV format) (annotations only for human samples)
- detection of structural variants (SVs), such as translocations, inversions as well as large and medium-sized indels (VCF and CSV format) including annotations (JSON and TSV format) (annotations only for human samples)
- metrices (CSV format)
Level 1:
- clipped sequencing data in FASTQ format
- if required, clipped sequencing data in BAM format can additionally be delivered
Level 2:
- mapping of the sequencing data (BAM and PBI format)
Level 3:
- calling of single nucleotide variants (SNVs) and small insertions and deletions (indels) (VCF format)
- calling of structural variations (SVs), including copy number variations (CNVs) (VCF format)
- annotation of variants (JSON and TSV format)
- phasing of variants (VCF and BAM format)
- repeat expansion analysis (VCF and BAM format)
Upon request, methylation analysis can also be performed for human samples. As the analysis options for HiFi WGS Flex strongly depend on the examined organism, we kindly ask you to get in contact with us so that we can discuss available options. Additionally, please feel free to contact us if you are interested in the de novo assembly of your sample.
Technical Information
At CeGaT, we are using sequencing technologies from Illumina and Pacific Biosciences (PacBio). For the products using the Illumina sequencing platforms, WGS samples are sequenced in 2 x 150 bp or 2 x 100 bp mode. Our PacBio platform enables us to sequence DNA fragments averaging 15-20 kb. If you require other sequencing parameters, please let us know! We can provide further solutions.
The output of a PacBio SMRT Cell depends on many factors, such as the DNA quality, the presence of inhibitors in the sample, or the movie time. Furthermore, it has been observed that sequencing libraries can influence each other in terms of the output generated per sample, even with equimolar pooling. The reasons for this observation are poorly understood, and even the technology provider, PacBio, cannot explain them. Therefore, the above-mentioned output values should be understood as approximate values.
Further Information about Genome Sequencing
Genome sequencing is also known as whole genome sequencing (WGS), full genome sequencing, or complete genome sequencing. Using this approach, the entirety of the genomic information is sequenced. Thus, the complete genome of a sample is analyzed at a single time. This means that in addition to the chromosomal DNA, the mitochondrial and, if available, the chloroplast’s DNA is sequenced. Whole genome sequencing is, thus, available for a variety of different organisms, including microorganisms, viruses, plants, and mammals, such as humans or mice.
With the development of high-throughput sequencing, formerly known as next-generation sequencing, the costs for whole genome sequencing dropped drastically, making research with whole genome sequencing possible and affordable. Whole genome sequencing has a variety of application areas. It can, for example, be used, to determine the mutation frequency in the complete human genome. Mutations occur naturally, e.g., due to replication errors during cell divisions, or DNA damaging and subsequent error-prone or insufficient repair mechanisms.
The mutation frequency is furthermore increased in cancer due to genomic instability. Altered mutation frequencies can be observed using whole genome sequencing. Another application area for whole genome sequencing includes genome-wide association studies, in which genetic variants or variants associated with a phenotype, e.g., a disease, are researched.
Whole genome sequencing is not only a powerful tool in the scientific field, it has also diagnostic applications. It can, for example, be used for diagnosing and treating diseases, including rare diseases, or detecting pathogens, and tracking outbreaks. With whole genome sequencing, personalized medicine is attainable and affordable to improve public health. In contrast to whole exome sequencing, whole genome sequencing also includes the intronic regions of a genome, and, thus, covers all coding and non-coding regions of the genome. This complete sequencing of the genome allows its more comprehensive assessment.
With whole genome sequencing getting faster, easier, and less expensive, it can contribute to your research today!
Our Commitment to You
Fast Processing
Turnaround time
≤ 15 business days
High Quality
Highest accuracy for all processes
Secure Delivery
Secure provision of sequenced data via in-house servers
Safe Storage
Safe storage of samples and data after project completion
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Contact Us
Do you have a question or are you interested in our service? Feel free to contact us. We will take care of your request as soon as possible.
Start Your Project with Us
We are happy to discuss sequencing options and to find a solution specifically tailored to your clinical study or research project.
When getting in contact, please specify sample information including starting material, number of samples, preferred library preparation option, preferred sequencing depth and required bioinformatic analysis level, if possible.
