Long Read Sequencing for Genome Assembly

The generation of high-quality genome assemblies is critical for their own comprehensive characterization and use as reliable reference sequences. Long-read sequencing is capable of generating long-read and ultra-long sequencing read lengths that span complex genomic regions, providing a more complete and structurally accurate genome. CD Genomics is a leading global life sciences company, and we are continually expanding our solutions and improving our available resources to help scientists accelerate their basic research. Based on our advanced PacBio SMRT sequencing and ONT Nanopore sequencing, and years of sequencing experience, we are committed to providing the best solutions to meet the project needs of our customers worldwide.

Introduction to Genome Assembly

Genome assembly is the process of combining your reads (short reads, long reads, or both) into long contiguous sequences (overlapping clusters). High-quality genome chromosome-scale sequences provide an important foundation for downstream analysis in genomics, especially haplotype resolution and construction of complete genomes, and play a key role in genome annotation, mutation detection, evolutionary analysis, gene function studies, comparative genomics, and more. Many different methods and tools exist to assemble genomes. However, genome assembly with short-read sequencing data is computationally demanding and often results in fragmented assemblies due to lack of sequence overlap. Accurate assembly of large structural variants, repetitive sequences, and GC-rich regions using short-read sequencing technologies is extremely challenging. The advent of long-read sequencing technologies has greatly improved the integrity of complex genome assemblies.

Fig. 1. Overview of the assembly process. (Zhang et al., 2022)

Solutions Offering at CD Genomics

CD Genomics provides cutting-edge long-read sequencing solutions tailored for the complexities of highly repetitive and multiplexed genomes. Our services go beyond traditional sequencing to expertly handle the most complex genomic regions, ensuring seamless alignment of every sequenced fragment, resulting in comprehensive and uninterrupted genome assemblies. This covers a broad spectrum, from tiny microbial genomes to the complex genomes of large plants, animals, and humans.

Our interdisciplinary team of experienced molecular biologists, cutting-edge genomics experts, and savvy bioinformaticians coordinate every phase of the project. This holistic approach encompasses everything from meticulous sample preparation and sequencing to nuanced data interpretation and analysis.

Advantages of Our Long Read Sequencing Solutions for Genome Assembly

• Our long-read sequencing technology generates read lengths spanning tens of kilobases, and sometimes more than a trillion bases. These extended read segments are invaluable in spanning repetitive regions, allowing the assembly of long read sequences.
• Read lengths can be optimized to suit specific genomic and assembly challenges by selecting segment sizes during sample preparation.
• High-coverage, long, and accurate HiFi reads combined with remote scaffolding technologies such as Hi-C not only accurately characterize complex genomic regions (e.g., large structural variants, repetitive sequences, and GC-rich regions), but also allow for the sequencing of much smaller microbial genomes in a single read length, completely eliminating the need for assembly.
• Simultaneous detection of base modifications and nucleotide sequences can be performed directly without amplification for more comprehensive genome analysis.
• Assemblers such as Canu, Flye, and Shasta are customized for long-read sequences and are designed to manage the higher error rates inherent in long-read sequencing technologies. We combine these advanced assemblers with proprietary algorithms to ensure the integrity and accuracy of genome assembly projects.

With its unparalleled expertise and cutting-edge technology, CD Genomics is a trusted partner in the genomics community, continually pushing the boundaries of what is possible in genome assembly and analysis. We aim to achieve seamless, telomere-to-telomere, and precise assembly of complex genomes on a truly routine basis. If you have any questions, please feel free to contact us. We look forward to working with you on projects of interest.

Related Services

PacBio SMRT Sequencing
Oxford Nanopore Sequencing
Human Whole Genome Sequencing
Animal/Plant Whole Genome De Novo Sequencing
Microbial Whole-Genome De Novo Sequencing