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Genomics in the long-read sequencing era
Trends in Genetics, 2023Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved.
Delphine Naquin, Claude Thermes
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Transcriptomics in the era of long-read sequencing
Nature Reviews GeneticsTranscriptome 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 +2 more
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Efficient short-read sequencing on long-read sequencers
2020We present SMURF-seq, a protocol to efficiently sequence short DNA molecules on a long-read sequencer by randomly ligating them to form long molecules. Applying SMURF-seq using the highly portable and inexpensive Oxford Nanopore MinION yields up to 30 fragments per read, providing an average of 6.2 and up to 7.5 million mappable fragments per run ...
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Amplicon Sequencing using the Long-Read Sequencing Technologies
Journal of Visualized ExperimentsThe 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 +7 more
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Transcript Identification Through Long-Read Sequencing
2021RNA-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 +4 more
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Long-read sequencing of new Drosophila genomes
Nature Reviews Genetics, 2021Kim 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
2021Isoform 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
2022Continuous 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, 2015The 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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