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Systematic comparative benchmarking of computational methods for the detection of transposable elements in long-read sequencing data

Seymen N, Santos R, Lakshmanan R, Topp S, Al-Chalabi A, Al Khleifat A, Breen G, Dobson RJ, Quinn JP, Karimi MM, Iacoangeli A.   +10 more
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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 ...
Carolina Monzó, Tianyuan Liu, Ana Conesa   +2 more
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Unveiling microbial diversity: harnessing long-read sequencing technology

Nature Methods
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing
Daniel P. Agustinho, Yilei Fu, Vipin K. Menon, Ginger A. Metcalf, Todd J. Treangen, Fritz J. Sedlazeck   +5 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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Genomics in the long-read sequencing era

Trends in Genetics, 2023
Long-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.
Erwin L, van Dijk, Delphine, Naquin, Kévin, Gorrichon, Yan, Jaszczyszyn, Rania, Ouazahrou, Claude, Thermes, Céline, Hernandez   +6 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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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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Transcript Profiling Using Long-Read Sequencing Technologies

2018
RNA sequencing using next-generation sequencing (NGS, RNA-Seq) technologies is currently the standard approach for gene expression profiling, particularly for large-scale high-throughput studies. NGS technologies comprise short-read RNA-Seq (dominated by Illumina) and long-read RNA-Seq technologies provided by Pacific Bioscience (PacBio) and Oxford ...
Anthony, Bayega, Yu Chang, Wang, Spyros, Oikonomopoulos, Haig, Djambazian, Somayyeh, Fahiminiya, Jiannis, Ragoussis   +5 more
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Long-Read Single-Cell Sequencing Using scCOLOR-seq

2023
Single-cell sequencing allows for the measurement of sequence information from individual cells with next-generation sequencing (NGS). However, its application to third-generation sequencing platforms such as Oxford Nanopore has been challenging because of its lower basecalling accuracy.
Martin, Philpott, Udo, Oppermann, Adam P, Cribbs   +2 more
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Modeling Methylation Patterns with Long Read Sequencing Data

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018
Variation in cytosine methylation at CpG dinucleotides is often observed in genomic regions, and analysis typically focuses on estimating the proportion of methylated sites observed in a given region and comparing these levels across samples to determine association with conditions of interest.
Karlene Nicole Meyer, Michelle R. Lacey
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