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Transcriptomics in the era of long-read sequencing

Nature Reviews Genetics
Transcriptome sequencing revolutionized the analysis of gene expression, providing an unbiased approach to gene detection and quantification that enabled the discovery of novel isoforms, alternative splicing events and fusion transcripts. However, although short-read sequencing technologies have surpassed the limited dynamic range of previous ...
Tianyuan Liu, Ana Conesa, Carolina Monzó   +2 more
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Amplicon Sequencing using the Long-Read Sequencing Technologies

Journal of Visualized Experiments
The World Health Organization (WHO) continues to emphasize the urgent need for a rapid, cost-effective, and user-friendly diagnostic method for tuberculosis (TB) and drug-resistant TB (DR-TB). Next-generation sequencing (NGS) technologies, endorsed by the WHO, have significantly improved the detection of DR-TB.
Morwasehla, Modjadji, Brendon Coenrad, Mann, Johannes, Loubser, Jennifer, Williams, Janré, Steyn, Elizabeth Maria, Streicher, Melanie, Grobbelaar, Robin Mark, Warren   +7 more
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Transcript Identification Through Long-Read Sequencing

2021
RNA-seq using long-read sequencing, such as nanopore and SMRT (Single Molecule, Real-Time) sequencing, enabled the identification of the full-length structure of RNA molecules. Several tools for long-read RNA-seq were developed recently. In this section, we introduce an analytical pipeline of long-read RNA-seq for isoform identification and the ...
Masahide, Seki, Miho, Oka, Liu, Xu, Ayako, Suzuki, Yutaka, Suzuki   +4 more
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Long-read sequencing of new Drosophila genomes

Nature Reviews Genetics, 2021
Kim et al. present a drosophilid genome resource comprising 101 de novo genome assemblies from 93 drosophilid species obtained by nanopore sequencing.
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Iso-Seq Long Read Transcriptome Sequencing

2021
Isoform sequencing (Iso-Seq), a long-read transcriptome sequencing method developed by Pacific Biosciences, has the capacity to generate full-length transcripts without the need for assembly. The method facilitates better genome annotation, identification of alternative splicing events, novel transcript isoforms and epi-transcriptome modification which
Hoang, Nam V., Henry, Robert J.
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Assembling Plant Genomes with Long-Read Sequencing

2022
Continuous improvements in long-read sequencing allow us to tackle increasingly big and complex genomes. Here we present the principles of long-read genome assembly, taking Solanum pennellii nanopore sequencing as an example.
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Genome sequencing: Long reads for a short plant

Nature Plants, 2015
The genome of a tiny resurrection plant has been sequenced using PacBio's long-read single-molecule real-time sequencing technology, aiding the understanding of extreme desiccation tolerance. The genome contiguity is comparable to that of genomes sequenced using far more laborious approaches.
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Method of the year: long-read sequencing

Nature Methods, 2023
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Profiling the epigenome using long-read sequencing

Nature Genetics
The advent of single-molecule, long-read sequencing (LRS) technologies by Oxford Nanopore Technologies and Pacific Biosciences has revolutionized genomics, transcriptomics and, more recently, epigenomics research. These technologies offer distinct advantages, including the direct detection of methylated DNA and simultaneous assessment of DNA sequences ...
Tianyuan Liu, Ana Conesa
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Long-read Sequencing Technology

This 50 minute lecture on long-read sequencing technology covers the following items: 1) Review of RNA-Seq Short-read Sequencing, 2) Overview and benefits of Long-read Sequencing, 3) Oxford Nanopore Sequencing, and 4) Pacific Biosciences Sequencing.
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