CD Genomics uses bioinformatics to provide GBS/RAD-seq sequencing data analysis service. We perform high-throughput genome-wide single nucleotide polymorphism (SNP) discovery and genotyping of multiple DNA samples simultaneously based on sequencing data by GBS/RAD-seq. Our unique skills in data analysis will exceed our clients' expectations on personalized data analysis and provide the most comprehensive data analysis results.
What Is GBS/RAD-seq Sequencing Data Analysis?
Next-generation sequencing (NGS) technologies have revolutionized the way we study and understand the genetic makeup of organisms. Among these technologies, sequencing genotyping (GBS) and restriction-site associated DNA sequencing (RAD-seq) utilize restriction enzymes to target specific regions of the genome, thereby reducing the complexity of libraries that can be sequenced using NGS platforms. These methods enable the discovery and genotyping of SNP across the genome, providing valuable insights into genetic diversity, population genetics and evolutionary studies. GBS/RAD-seq sequencing data analysis involves the processing, analysis and interpretation of large-scale sequencing data generated by these techniques.
Fig. 1. Schematic presentation of a GBS application for plant genetic diversity analysis. (Peterson G W, et al, 2014)
We Can Help Our Clients With:
The results of bioinformatic analysis of GBS/RAD-seq sequencing data can be used in the following research fields:
Co-dominant SNP genotyping
Genetic diversity analysis
Gene mapping
QTL mapping
Batch segregation analysis
Mapping to whole genome sequences
Discovery of (rare) SNP variants
Genome-wide association mapping
Genomic selection/prediction
CD Genomics Data Analysis Pipeline:
At CD Genomics, we have developed a comprehensive data analysis process specifically tailored for GBS and RAD-seq sequencing data. Our expert team combines cutting-edge bioinformatics tools and custom algorithms to ensure accurate and efficient analysis of raw sequencing data. From data pre-processing and quality control to variant detection and genotype inference, our process covers all the essential steps in GBS/RAD-seq data analysis.
Reference-Based and De Novo Analysis
Our analysis process supports both reference-based and ab initio approaches to meet different research needs. In the presence of a reference genome, we can map sequencing reads to the reference genome and perform SNP calling and genotyping. For species without a reference genome, our ab initio analysis approach is able to identify several pairs of nearly identical reads representing alternative alleles at the locus.
Customized Analysis Strategies for Polyploid Organisms
Due to the complexity of genomes, polyploid organisms present unique challenges in GBS/RAD-seq data analysis. CD Genomics has developed novel and rigorous statistical methods for predicting the number of sequence reads needed to ensure accurate polyploid genotyping. Our expertise in handling polyploid data allows us to provide tailored analysis strategies and overcome the complexities associated with polyploidy.
Bioinformatics Support and Variant Analysis
Our team of bioinformatics experts at CD Genomics provides comprehensive support for GBS/RAD-seq data analysis. We provide services ranging from sequence pre-processing, alignment and variation analysis to interpretation of genetic markers. By leveraging advanced bioinformatics tools and algorithms, we can efficiently analyze large-scale sequencing data, discover meaningful genetic variation, and provide valuable insights into genetic diversity, population structure, and evolutionary patterns.
GBS/RAD-seq Sequencing Data Analysis Content:
| 1. Raw sequence data acquisition. |
2. Data pre-processing and quality control. |
| 3. Variant detection and genotype inference. |
4. SNP filtering and annotation. |
| 4. SNP filtering and annotation. |
6. Genetic diversity analysis. |
| 7. Phylogenetic analysis. |
8. Data visualization. |
How It Works
CD Genomics is a high-tech company specializing in multiomic data analysis. We provide services such as project design, data analysis, and database construction. With a focus on developing breakthrough products and services, we are a pioneer in the biotechnology industry, serving researchers and partners worldwide.
CD Genomics provides general analysis and customized analysis of GBS/RAD-seq sequencing data. If you are interested in our services, please contact us for more detailed information.
Reference
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Peterson G W, Dong Y, Horbach C, et al. Genotyping-by-sequencing for plant genetic diversity analysis: a lab guide for SNP genotyping[J]. Diversity, 2014, 6(4): 665-680.
