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Genome Assembly Service

Genome Assembly Service

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Our bioinformatics pipelines can handle data generated from different sequencing technologies such as Illumina, MGI, PacBio, and ONT. Our in-house genome assembly and annotation pipeline can be used to generate chromosome-level contigs, as well as manually managed annotation pipelines, making your submitted datasets immediately available.

What is Genome Sequence Assembly?

Genome Sequence Assembly is a computational method used to merge small fragments of DNA sequences obtained from sequencing methods to form longer DNA sequences and ultimately to reconstruct the primitive genome. This is done by analyzing the overlaps between these fragments and merging them to form larger fragments. The goal of De novo assembly algorithms is to form a new, previously unknown sequence.

De novo genome assembly can be performed in two ways:

  • In a map-based fashion, where an existing backbone sequence is used, and the assembly algorithm builds a new sequence that is similar but not identical to the backbone sequence.
  • In a de novo fashion, where the genome is assembled without the aid of a reference genome. In this case, the assembly algorithm has to computationally find overlaps between reads and try to assemble them correctly.

Genome assembly is particularly useful when studying organisms whose genomes have not been sequenced before or when studying the genomes of organisms with high levels of genetic diversity. At CD Genomics, we offer genome assembly services to help researchers assemble and analyze the genomes of various organisms using advanced sequencing technologies and bioinformatics tools.

Genome Assembly PipelineGenome Assembly Pipeline

Genome Assembly Services Packages

CD Genomics has well-established genome sequencing, assembly and annotation services and has extensive experience in genome projects at different levels of conventional genomes, haplotype genomes, and (near) complete genome maps. We offer different customized services for different projects, species, and genome assembly level needs.

De Novo Genome Assembly Service

Our de novo genome assembly service delivers a comprehensive set of deliverables to our clients. We aim to enable our partners to analyze the genome of their organism of interest at a high level of detail.

Conventional Genome Assembly Service

Sequencing Platform Recommended Depth Note
NGS reads ~ 50x Need to be determined by specific projects and species
PacBio HiFi reads ~ 30x
Hi-C ~ 100x

Complete Genome Assembly Service

Sequencing Platform Recommended Depth Note
NGS reads 50x - 100x Need to be determined by specific projects and species
ONT ultra-long reads 80x - 100x
PacBio HiFi reads 30x - 60x
Hi-C ~ 100x

Haploid Genome Assembly Service

Currently, most diploid genome assemblies ignore the differences between homologous chromosomes and assemble the genome into a pseudo-haploid sequence, which is an artificial consensus for diploid-type assemblies. This artificial consensus may lead to inaccurate gene annotation and errors in biological interpretation. The quality of haploid genome sequence assembly has a direct impact on downstream genome analysis, especially in genome variation detection, genome annotation, gene regulatory element analysis, evolutionary analysis, etc.

CD Genomics provides haploid genome assembly services, including haplotyping, according to clients' needs.

Maximize Your Haploid Genome Assembly Project:

  • Distinguish genetic information from different parental chromosomes and gaining insight into the biology of a single chromosome or a specific chromosomal region can help to study the pathogenesis of genetic diseases and scientific issues such as plant hybrid advantage.
  • Explore the transcription factor binding motif genetic variation occurring on chromosomes and its possible allele-specific expression, and gain insight into the upstream regulatory elements and chromatin states of specific expression and their molecular mechanisms.
  • Explore the allele-specific expression that may result from differences in genetic variation on chromosomal regulatory elements of different parental origins.
  • Explore allele-specific expression caused by structural differences between homologous chromosomes.

Polyploid Genome Assembly Service

Polyploidy research relies heavily on a high-quality genome. polyploid organisms are common in both plants and animals, and their genomes can be complex and challenging to assemble due to the Genome mining of heterozygous and homozygous polyploid species can contribute to research areas such as the evolution of genome structure and its mechanisms of action on species differentiation and phenotypic trait formation.

CD Genomics provides comprehensive polyploid genome assembly services and has helped clients to:

  • Compare gene content, GC content, gene structure, distribution of repetitive elements, etc., and structural variation (inversions, translocations) between subgenomes, combined with TE distribution, etc. for inter-subgenomic (homologous chromosomal) variation analysis.
  • Dissect asymmetric evolutionary mechanisms in polyploid species.
  • Focus on and resolving the evolutionary history of species.
  • Explore epistatic regulatory differences between homologous chromosomes, such as chromatin dynamics, histone modifications, etc., combining with our data analysis services such as Hi-C and ChIP-Seq.

Mitochondrial Genome Assembly

To solve the problem of difficult organelle genome assembly due to complex structural changes and long segments of repetitive DNA, CD Genomics provides a one-stop mitochondrial genome assembly service to help customers extract and assemble mitochondrial genome sequences from massive amounts of whole genome data.

We Can Help Our Clients with

  • Detect common and rare mitochondrial point mutations and deletions.
  • Rapid analysis of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA).
  • Accurately and sensitively measure heterogeneity.
  • Analysis of the highly variable region of the D-loop and/or the entire mitochondrial genome.

Project Deliverables of Our Genome Assembly Service

  • The main deliverable is in FASTA format, which is the final assembled genome that has been generated using our advanced sequencing technologies and bioinformatics tools.
  • We also provide BAM files containing alignments mapped to the draft assembly. This helps in identifying and analyzing structural variations, such as insertions, deletions, and inversions.
  • Our QC report provides an assessment of the quality of the assembly and the accuracy of the results. This report also includes information on the completeness of the assembly, such as the number of complete genes and the number of missing genes.
  • If applicable, our Genome Annotation deliverables include a genome annotation file in GFF3 format, predicted gene CDS sequences in FASTA format, predicted gene peptide sequences in FAST format, and alignment files from RNA-seq and Iso-Seq data in BAM format. We also provide a repeat annotation file in GFF3 format and visualization of structures of manually curated genes.

Why Choose Our Genome Assembly Service

  • Years of genome sequencing and assembly experience
  • Unique internal assembly pipeline, combining high integrity and high accuracy
  • One-stop analysis service from pre-protocol design to genome sequencing and personalized analysis
  • Rigorous in-house genome assembly treatment evaluation system. Includes evaluation process for covering multiple aspects of continuity, completeness, accuracy, heterozygosity, organelle genomes, etc.

How It Works

Initial Consultation

Initial Consultation

  • Meet with technical experts to understand the client's research goals and objectives
  • Discuss project design and scope of work
  • Determine sample preparation and sequencing requirements
  • Provide an estimated schedule and budget

Project Confirmation

Project Confirmation

  • If you don't have data yet, we can also provide omics sequencing services
  • Project confirmation process

Data Analysis

Data Analysis

  • Perform quality control and data filtering
  • Align the reads to the reference genome
  • Identify and annotate genetic variants or gene expression levels
  • Perform downstream analysis such as functional annotation, pathway analysis, or gene network analysis

Deliverables

Results Delivery

  • Provide the client with a detailed report summarizing the analysis results
  • Include visualizations of the data, such as heat maps, scatter plots, or volcano plots
  • Provide recommendations for future research directions
* For Research Use Only. Not for use in diagnostic procedures.
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