Gold Standard Genome

Gold-Standard Genome Assembly

Our Gold-Standard Genome Assembly workflow is designed to generate chromosome-scale, highly accurate reference genomes by integrating multiple complementary sequencing technologies. Rather than relying on a single data type, we combine the strengths of long-read sequencing, chromatin conformation capture, optical genome mapping, and transcriptomic evidence to produce assemblies with exceptional continuity, structural accuracy, and gene completeness.

Our Integrated Multi-Omics Assembly Strategy

PacBio HiFi Sequencing
 

PacBio HiFi reads serve as the foundation of the assembly process. Their long read length and >99.9% base accuracy enable the resolution of repetitive regions, structural variants, and complex genomic architectures while producing highly contiguous primary assemblies.

Hi-C Sequencing
 

Hi-C chromatin interaction data is used to scaffold contigs into chromosome-scale assemblies. The long-range interaction information accurately orders and orients contigs, resolves misassemblies, and reconstructs complete chromosomes that closely represent the native genome organization.

Bionano Optical Mapping
 

Bionano optical maps provide an independent, genome-wide structural validation of the assembly. Optical mapping helps identify and correct structural inconsistencies, resolve large repeats, improve scaffold continuity, and validate chromosome architecture, resulting in a highly reliable final assembly.

Illumina RNA-Seq
 

RNA-Seq data provides comprehensive transcriptome evidence for gene prediction and functional annotation. Transcript alignments support accurate exon-intron boundary identification, improve gene model construction, and facilitate downstream functional analyses.

PacBio Iso-Seq
 

Full-length Iso-Seq transcripts capture complete transcript isoforms without the need for transcript assembly. Iso-Seq significantly improves annotation accuracy by identifying alternative splicing events, untranslated regions (UTRs), novel transcripts, and complete gene structures.

Comprehensive Assembly Validation

To ensure the highest assembly quality, multiple validation and quality assessment approaches are employed throughout the workflow, including:

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• • Genome completeness assessment using BUSCO

• • Consensus accuracy evaluation using k-mer-based analyses

• • Structural validation using optical mapping and Hi-C contact maps

• • Telomere and centromere assessment for chromosome completeness

• • Assembly statistics including contig/scaffold N50, L50, genome size, gap content, and chromosome continuity

• • Detection and correction of potential misassemblies through iterative refinement

Deliverables

Our Gold-Standard Genome Assembly service includes:

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• • Chromosome-scale reference genome assembly

• • Structurally validated scaffolds

• • Quality assessment and assembly statistics

• • Assembly completeness reports

• • Hi-C contact maps and scaffolding reports

• • Bionano structural validation reports

• • Repeat annotation

• • Comprehensive structural and functional genome annotation supported by RNA-Seq and Iso-Seq evidence

• • Gene, transcript, protein, and coding sequence datasets

• • Final publication-ready genome assembly with associated quality metrics

Applications

Our Gold-Standard Genome Assemblies support a wide range of research and breeding applications, including:

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• • De novo genome assembly

• • Comparative genomics

• • Evolutionary and population genomics

• • Pan-genome construction

• • Functional genomics

• • Marker discovery and genomic selection

• • Structural variation analysis

• • Gene family evolution

• • Crop improvement and breeding

• • Conservation genomics

• • Precision agriculture and biotechnology

By integrating PacBio HiFi, Hi-C, Bionano Optical Mapping, Illumina RNA-Seq, and PacBio Iso-Seq into a unified assembly workflow, we deliver reference genomes with exceptional continuity, completeness, structural accuracy, and annotation quality — providing a robust genomic resource for both fundamental research and translational applications.