PacBio Sequencing and Its Applications

By Anthony Rhoads, Kin Fai Au. Genomics, Proteomics & Bioinformatics, 2015

1,999 citations recorded by the source corpus.

Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing (SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with diseases. Moreover, PacBio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes, due to its ability to sequence full-length transcripts or fragments with significant lengths. Additionally, PacBio’s sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using PacBio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with PacBio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. The advent of PacBio sequencing has made available much information that could not be obtained via SGS alone.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/2125bf4c0ccb9623d26d0790e65e1276e2f13f56

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Citations in the corpus

Falco: high-speed FastQC emulation for quality control of sequencing data (2019, positive): “The sentence “While FastQC is capable of making summaries for protocols such as 454 27 PacBio 28 , which generate sequences with around 10,000 bases per read ” should be updated to "While FastQC is capable of making summaries for protocols such as 454 27 PacBio 28 , which generate sequences with aro”
Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing (2021, background): “Nevertheless, significant drawbacks include the relatively high error rate (up to 15% per sequence) (28, 29), limited applicability in high-throughput studies, higher”
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities (2020, neutral): “On a case-by-case basis, errorcorrected unassembled data generated by long-read sequencing technologies, such as PacBio (6) and ONT (7) can be also supported.”
RNA-Seq methods for transcriptome analysis (2016, neutral): “Single-molecule real-time sequencing (SMRT) on the PacBio sequencing platform offers long reads up to 5 kb.(70) However, this method is costly, and has a high error-rate and low multiplexing capacity.”
Nanopore sequencing technology, bioinformatics and applications (2021, methodology): “Data quality can be improved by sequencing each dsDNA multiple times to generate a consensus sequence, similar to the ‘circular consensus sequencing’ strategy used in the other single-molecule long-read sequencing method from Pacific Biosciences (PacBio) 39 .”
RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis (2018, background): “This is, however, not currently the case, both due to fragmentation and degradation of template molecules during library preparation and because of early termination of the sequencing, which leads to ambiguities in transcript identification [223].”
Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer (2016, background): “…clear that certain lncRNAs can associate with chromatin-modification complexes to carry out cellular functions. lncRNAs in chromatin looping in cancers Another mechanism of action by which lncRNAs function to regulate transcription is via enhancer lncRNAs (eRNAs) associated with chromatin loops.”
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center (2016, methodology): “To simplify this task, PATRIC integrates the Assembly RAST (ARAST) service to enable researchers to assemble short reads that are single or paired-end (typically from Illumina), and also long reads that include bax.h5 read files and filtered FASTQ files from PacBio (9) and Oxford Nanopore (10,11).”
Microbial Biodiversity and Bioremediation Assessment Through Omics Approaches (2020, methodology): “It employs a framework made of several SMRT cells which comprises microfabricated nanostructures called zero-mode waveguides (ZMWs) (Rhoads and Au, 2015).”
Generations of Sequencing Technologies: From First to Next Generation (2017, methodology): “It uses a structure composed of many SMRT cells, each cell contains microfabricated nanostructures called zeromode waveguides (ZMWs) which are wells of tens of nanometers in diameter microfabricated in a metal film which is in turn deposited onto a glass substrate [44,45].”
Overview of Next Generation Sequencing Technologies (2018, background): “…cytosine methylations, change the IPD and thus can be identified as a modified base (Fang et al., 2012; Flusberg et al., 2010; Murray et al., 2012; Rhoads & Au, 2015; Vilfan et al., 2013; Zhang, Sun, Menghe, & Zhang, 2015; see https://s3.amazonaws.com/files.pacb.com/png /basemod_benefits_lg.png).”