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The Basics and Beyond of PacBio SMRT Sequencing

This is a comprehensive guide to PacBio sequencing, covering everything from the basics to more advanced topics.

PacBio Sequencing Empowers Mitochondrial Genome Research

Many mitochondrial genomes have been deciphered, and the importance of mitogenomes has been gradually explored.

Pan-Genome Analysis: Overview, Workflow, Application and Recent Advances

A pan-genome is the sum of all genomic information within a species. Pan-genomes have potential applications in crop improvement, evolution and biodiversity research.

Long-Read 101: Nanopore Full-Length Transcriptome Sequencing

Nanopore full-length transcriptome sequencing is an innovative technique that utilizes Oxford Nanopore Technologies' (ONT) sequencing platform to obtain comprehensive and uninterrupted

Nanopore Sequencing 101: Bioinformatics Analysis of ONT Data

Oxford Nanopore Technologies (ONT) sequencing has witnessed significant progress in recent years, becoming a key player in the genomics field.

Nanopore Sequencing 101: Choosing the Right Sequencing Device

Oxford Nanopore's technology empowers base modification analysis and nucleotide sequencing within a single read-length fragment...

Nanopore Sequencing 101: Library Construction

Library construction is indeed a critical step in the DNA sequencing process, especially in nanopore sequencing...

Overview of Nanopore Sequencing

Nanopore sequencing, a pivotal component of long-read sequencing technology, has emerged as a formidable and promising approach in the realm of genomics and molecular biology.

Single-Molecule Real-Time Sequencing in cfDNA Analysis

Circulating free DNA (cfDNA) refers to fragmented DNA molecules that cells release into the bloodstream.

Troubleshooting SMRTbell Library Sequencing Performance

The success of SMRTbell library sequencing relies on the quality of the starting material. Factors such as DNA damage.

Copy Number Variation Analysis

Copy number variation (CNV) is a genomic alteration phenomenon that can lead to copy number abnormalities in one or more genes involved in the process of evolutionary adaptation, genomic disease, and disease progression.

Introduction to The Complete Sequence of a Human Genome

The human genome, the genetic code that makes us uniquely human, has been the subject of scientific study and fascination for decades. The human genome contains approximately 3.055 billion base pairs.

Long-read Sequencing Reveals Unseen Genomic Variants

A complete map of genomic variation is important to gain insight into genetic characterization and to aid in precision disease research, which can further address research areas such as evolution, agriculture, and medicine.

PacBio SMRT Sequencing for Human Telomere Sequence

Telomeres are specialized nucleoprotein structures at the ends of linear chromosomes, and the ends of human chromosomes are covered by telomeres.

Pore Occupancy: Definition, Improving Pore Occupancy

Pore occupancy is a key determinant of sequencing efficiency and directly impacts the speed and success of data acquisition in the Oxford Nanopore Sequencing Technology Platform.

Saturated Pores for Nanopore Operation

A very useful diagnostic of a nanopore run is the state of the pores: whether they are being sequenced ("single pore"), saturated, unavailable, or multiple. Saturated pores pile up and cannot be sequenced.

Telomere-to-telomere Gapless Genome Assembly

Telomere-to-telomere genome assembly refers to the generation of complete chromosomal DNA sequences without any gaps from one end of the chromosome (telomere) to the other.

What is a Consensus Sequence?

Organisms have similar and different characteristics. The genome or genetic composition of an organism is important when studying the relationships between organisms and categorizing them. Gene sequences can change at any time.

What is the RNA Integrity Number (RIN)?

RIN is a numerical value that indicates RNA integrity. Technically, it applies to microfluidic chip-based isolation and allows us to visualize bands and measure integrity values by calculation and using mathematical models.

Alternative Splicing Analysis

Alternative splicing is a complex cellular mechanism that is critical for proteome diversification and plays an important role in cellular development, function, and disease mechanisms.

Conservation Genomics

Conservation genomics is an emerging interdisciplinary field that harnesses the power of genomics to gain insights into biodiversity, species differentiation, and the evolutionary processes that influence species survival.

Full-Length 16S Sequencing

Characterizing microbial communities in specimens is one of the main goals of microbiome research. The 16S ribosomal RNA (rRNA) gene is approximately 1.5 kb in length and contains several conserved and highly variable regions (V1-V9) that vary between bacteria.

Fusion Transcript Sequencing

Fusion genes are caused by chromosomal aberrations such as translocations, duplications, inversions or small interstitial deletions. At the transcript level, fusion genes may not only reflect underlying genomic rearrangements, but may also arise as a result of aberrant transcription or trans-splicing events.

Generate Genome Assemblies Using Long Sequencing Reads

De novo genome assembly is the process of splicing DNA fragments into contiguous segments (overlapping clusters) representing the chromosomes of an organism.

Improving the Accuracy of Nanopore Sequencing

Oxford Nanopore continues to drive further performance enhancements by iteratively iterating on its technology to improve the accuracy of raw reads.

Long-read Sequencing for Crop Genomics and Improvement

The advent of long-read sequencing technologies has led to tremendous advances in crop genomics, and they help researchers provide comprehensive sequence data by detecting high-quality reference genomes.

Long-read Sequencing for Livestock Genomics and Breeding

Long-read sequencing technology is helping researchers and breeders produce healthier, more productive livestock. Agricultural genomics has and will continue to drive sustainable productivity and provide solutions to the growing challenges facing the global population.

Long-read Sequencing for Population-scale Genomic Study

Population genetics and precision health research rely on large genomic datasets. Long-read sequencing from Pacific Biosciences and Oxford Nanopore Technologies (ONT) has achieved a level of accuracy and throughput that allows for the progression from single genomes and small populations of individuals to the detection of variation in large-scale populations.

Methods and Tools for Assessing the Quality of Genome Assemblies

With the rapid development of sequencing technologies, especially the maturation of long-read sequencing technologies (Pacific Biosciences and Oxford Nanopore sequencing), the number and quality of published genome assemblies have significantly increased.

Nanopore Basecalling

Basecalling, the computational process of converting raw electrical signals into nucleotide sequences, is often the first step in analyzing nanopore sequencing signals and is critical for Nanopore sequencing platforms.

Repeat Expansions Analysis

Repeat expansion, a structural variation in which the number of tandem DNA sequences doubles, has long been associated with many genetic and neurological disorders. However, despite the well-documented contribution of tandem repeats (TRs) to genetic variation, TRs remain poorly understood and their impact on phenotypes and disease may be underestimated.

Single Nucleotide Variants Analysis

Single nucleotide variants (SNVs) occur when a single nucleotide in the DNA sequence (e.g., A, T, C, or G) is altered. SNVs are the most common type of sequence change in the human genome and play an important role in disease susceptibility and an individual's response to therapy.

Structural Variation Analysis

Structural variants (SVs) represent significant alterations in DNA beyond the length of typical single nucleotide polymorphisms. As the largest variation in the human genome, SVs are closely associated with human diseases (e.g., hereditary disorders and cancer), evolution (e.g., gene loss and transposon activity), gene regulation (e.g., rearrangement of transcription factors), and other phenotypes (e.g., mating and intrinsic reproductive isolation).

Challenges in Defining mRNA Transcript Boundaries Using Long-Read Sequencing

The quest to decipher the intricacies of gene expression has taken a remarkable leap forward with the emergence of long-read sequencing technologies. By providing unprecedented insights into the full length of mRNA transcripts, these technologies promise to revolutionize our understanding of genetic regulation, alternative splicing, and isoform diversity.

Nanopore Adaptive Sampling Revolutionizes Target Enrichment

In a groundbreaking advancement for genomics, the concept of Nanopore Adaptive Sampling has emerged as a transformative strategy, pushing the boundaries of target enrichment. This novel approach introduces a paradigm shift by seamlessly integrating target enrichment or depletion directly into the sequencing process.

Contigs and Scaffolds in Genome Assemblies

Both contigs and scaffolds are nucleotide sequences that are reconstructed in a genome sequencing project. Contig is a continuous piece of genomic sequence containing A, C, G, and T bases without gaps. A scaffold is a genomic sequence composed of contigs. Thus, the shortest assembled component is the contig, and scaffolds are combinations of contigs.

Long-read Genome Sequencing of Fireflies

Bioluminescence is a particularly interesting phenomenon, and its origin and evolution have long fascinated biologists. Fireflies (Lampyridae) are one of the best-known luminescent organisms, and thus an important subject of scientific studies, especially related to their bioluminescent behavior and biochemistry. Together with other luminous beetles, such as Rhagophthalmidae, Phengodida e, and some Elateridae. Fireflies pass Luciferase catalyzes luciferin for bioluminescence.

Long-read Sequencing for DNA 5-methylcytosine (5mC) Analysis

5-methylcytosine (5mC) is the most common form of DNA methylation and is involved in regulating many biological processes. Recent long-read length sequencing technologies, including Oxford Nanopore sequencing and PacBio HiFi sequencing, have dramatically expanded the ability to detect long-range, single-molecule, and direct DNA modifications without the need for additional laboratory techniques.

Long-read Sequencing for Microbiome Metagenomics

Overview of Long-read Sequencing

Long-read sequencing has emerged as a breakthrough method in the field of genomics, providing unrivaled insights into the complexity of genomes. While traditional short-read methods have proven limited in some cases, long-read sequencing has paved the way for a more comprehensive understanding of genetic structure and function.

PacBio HiFi Metagenomics

Metagenome sequencing has historically been a challenging endeavor. The inherent complexity of microbial communities means that any sequencing technology must provide both breadth (to capture entire communities) and depth (to understand individual species). This balance is critical for reconstructing the accurate genome of each member, especially those that are less abundant or uncultured.

PacBio HiFi Sequencing for Spinal Muscular Atrophy Analysis

Spinal muscular atrophy (SMA) has long been recognized as a serious neuromuscular disease, is currently ranked as the leading cause of early infant mortality, and is one of the most common recessive diseases worldwide. Two genes play a role in the onset and severity of SMA: SMN1 and SMN2. SMN1 is highly homologous to its paralog SMN2.

PacBio HiFi Sequencing

PacBio sequencing technology has evolved to a different type of long read, known as highly accurate long reads, or HiFi reads. PacBio, the only sequencing technology to offer HiFi reads, is 99.9% accurate, comparable to short reads and Sanger sequencing. With HiFi reads, you no longer need to sacrifice long read lengths for high-precision sequencing to solve the toughest biological problems.

PacBio Long-read Isoform Sequencing (Iso-Seq)

PacBio SMRT long-read isoform sequencing (Iso-Seq) is revolutionizing the way transcriptomes are analyzed, advancing our understanding of selective splicing events, post-transcriptional modifications and gene regulation. These methods offer many advantages over the most widely used high-throughput short-read RNA sequencing (RNA-Seq) methods and allow a comprehensive analysis of the transcriptome to identify full-length splicing isoforms and several other post-transcriptional events.

PacBio SMRT Sequencing for Methicillin-Resistant Staphylococcus aureus (MRSA)

Staphylococcus aureus is a Gram-positive, non-motile, coagulase-positive globular bacterium of the phylum Thicket. Although the genus Staphylococcus includes 52 species and 28 subspecies, S. aureus is by far the most clinically relevant. Staphylococcus aureus is present in 20-40% of the nasal mucosal commensal microbiota of the general population.

Transcriptome Analysis of Human Breast Cancer Cell Lines MCF-7

It is well known that cancer is caused by the gradual accumulation of genomic and epigenomic alterations leading to dysregulated cell growth. Chromosomal instability (a hallmark of cancer) greatly contributes to the process of oncogenesis and subsequent cancer progression, with continuous mutations in the genome and epigenome of each cancer cell leading to a diverse transcriptome in cancerous tissues.

High-Molecular-Weight DNA Extraction for Long-Read Sequencing

Long-read sequencing technology requires high molecular weight DNA of sufficient purity and integrity because the quality of the DNA starting material will be directly reflected in the sequencing results. Any irreversible DNA damage present in the input material (e.g., interstrand cross-links, etc.) will result in compromised performance and reduced read length.

Long-read Genome Sequencing of Bats

With more than 1,400 species identified to date, bats (Chiroptera) account for about 20% of all extant mammal species. bats are found throughout the world and successfully occupy different ecological niches. From the smallest bumblebee bat (Craseonycteris thonglongyai) to the large (1 kilogram) golden-topped fruit bat (Acerodon jubatus), they possess extraordinary adaptations, including flight, echolocation, extremely long lifespans, and a unique immunity that both fascinates and frightens people.

Long-read Sequencing for Haplotype Phasing

Humans and most other animals are diploid, meaning that each cell carries two copies of the individual genome in its nucleus, one from its mother and one from its father. Many plants have high ploidy; for example, the hexaploid California redwood has six copies of each chromosome. The number of complete sets of chromosomes (or haplotypes) in each cell is called ploidy.

Long-read Sequencing for Viral Genomes Study

The importance of viruses in community composition and nutrient cycling in various ecosystems, including soil, is increasingly recognized. In addition, the COVID-19 pandemic brought a sudden urgency to virus research, prompting many to look more deeply into all the tools available to characterize viral genomes. Historically, studies of viral genomes have relied heavily on short-read sequencing.

Long-read Whole Genome Sequencing

A large number of genetic variations and somatic mutations exist within human, plant, animal, or microorganism genomes. Genetic variation is associated with disease risk and phenotypic variation between individuals. In recent years, whole-exome sequencing (WES) has been a popular method for identifying the genetic basis of disease in research and clinical settings.

Maize Genome Complexity Traversed with Long-read Sequencing

Maize is one of the most important crops in the world and has a long history as a classical model organism in genetic research. Maize is known for its excellent chromosome cytology and rich history of transposon studies. They are diploids with 10 chromosomes, and transposons make up the bulk of the maize genome (about 85%).

Revio Long-read Sequencing System Performance Enhancements

Since its introduction, Pacbio SMRT sequencing technology has gained attention for its advantages of long reads (10-25k), single molecules, and no GC preference. In 2019, PacBio launched HiFi sequencing, which increases single-molecule sequencing accuracy to 99.9% (Q33). And now, the next-generation, high-throughput Revio system, launched in 2022, breaks through the throughput limit once again.

Newest Whole Genome Sequencing Trends in 2024

For research purposes only, not intended for personal diagnosis, clinical testing, or health assessment