Opportunities and challenges in long-read sequencing data analysis

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<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

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limma powers differential expression analyses for RNA-sequencing and microarray studies

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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Salmon provides fast and bias-aware quantification of transcript expression

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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

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Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint

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Assembly of long, error-prone reads using repeat graphs

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Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

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Alternative isoform regulation in human tissue transcriptomes

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Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

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Coming of age: ten years of next-generation sequencing technologies

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Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

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Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

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Accurate whole human genome sequencing using reversible terminator chemistry

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Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

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A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands

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Performance of neural network basecalling tools for Oxford Nanopore sequencing

Wick, R. R., Judd, L. M., & Holt, K. E. (2019) · Genome Biology · doi:10.1186/s13059-019-1727-y · Cited by 3,221

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

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Fast and accurate de novo genome assembly from long uncorrected readsPreprint

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The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

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An integrated semiconductor device enabling non-optical genome sequencing

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A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

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Nanopore sequencing and assembly of a human genome with ultra-long reads

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Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

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m6A RNA methylation promotes XIST-mediated transcriptional repression

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The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

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Direct detection of DNA methylation during single-molecule, real-time sequencing

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The sequence of sequencers: The history of sequencing DNA

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Fast and accurate long-read assembly with wtdbg2

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Detecting DNA cytosine methylation using nanopore sequencing

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Mapping copy number variation by population-scale genome sequencing

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Reversible methylation of m6Am in the 5′ cap controls mRNA stability

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Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

Berlin, K., Koren, S., Chin, C.-S., Drake, J. P., Landolin, J. M., & Phillippy, A. M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3238 · Cited by 947

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

Arango, D., Sturgill, D., Alhusaini, N., Dillman, A. A., Sweet, T. J., Hanson, G., Hosogane, M., Sinclair, W. R., Nanan, K. K., Mandler, M. D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.030 · Cited by 862

Whole-genome re-sequencing

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5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming

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Resolving the complexity of the human genome using single-molecule sequencing

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Nanopore native RNA sequencing of a human poly(A) transcriptome

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Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

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Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

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Structural variant calling: the long and the short of it

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A single-molecule long-read survey of the human transcriptome

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Assessment of transcript reconstruction methods for RNA-seq

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From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy

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Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

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Structural variation in the sequencing era

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A survey of the sorghum transcriptome using single-molecule long reads

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Improved reference genome of Aedes aegypti informs arbovirus vector control

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The advantages of SMRT sequencing

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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

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N6-methyl-adenine: an epigenetic signal for DNA–protein interactions

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Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

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Accurate detection of m6A RNA modifications in native RNA sequences

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Mapping DNA methylation with high-throughput nanopore sequencing

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The birth of the Epitranscriptome: deciphering the function of RNA modifications

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Characterizing the Major Structural Variant Alleles of the Human Genome

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SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantificationPreprint

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The advantages of SMRT sequencing

Roberts, R. J., Carneiro, M. O., & Schatz, M. C. (2013) · Genome biology · doi:10.1186/gb-2013-14-7-405 · Cited by 454

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

Koren, S., & Phillippy, A. M. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.11.014 · Cited by 422

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

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A robust benchmark for detection of germline large deletions and insertions

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Ordered Restriction Maps of Saccharomyces cerevisiae Chromosomes Constructed by Optical Mapping

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Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

Gordon, S., Tseng, E., Salamov, A. A., Zhang, J., Meng, X., Zhao, Z., Kang, D., Underwood, J. G., Grigoriev, I. V., Figueroa, M., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0132628 · Cited by 410

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

Cretu-Stancu, M., van Roosmalen, M. J., Renkens, I., Nieboer, M. M., Middelkamp, S., de Ligt, J., Pregno, G., Giachino, D. F., Mandrile, G., Valle-Inclán, J. E., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01343-4 · Cited by 403

Long reads: their purpose and place

Pollard, M., Gurdasani, D., Mentzer, A. J., Porter, T., & Sandhu, M. S. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy177 · Cited by 391

The Expanding Landscape of Alternative Splicing Variation in Human Populations

Park, E., Pan, Z., Zhang, Z., Lin, L., & Xing, Y. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.11.002 · Cited by 385

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

Byrne, A., Beaudin, A. E., Olsen, H. E., Jain, M., Cole, C., Palmer, T., DuBois, R. M., Forsberg, E. C., Akeson, M., & Vollmers, C. (2017) · Nature Communications · doi:10.1038/ncomms16027 · Cited by 379

Mechanism and Function of Oxidative Reversal of DNA and RNA Methylation

Shen, L., Song, C., He, C., & Zhang, Y. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060713-035513 · Cited by 369

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

Gupta, I., Collier, P. G., Haase, B., Mahfouz, A., Joglekar, A., Floyd, T., Koopmans, F., Barres, B., Smit, A. B., Sloan, S. A., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4259 · Cited by 343

Characterization of the human ESC transcriptome by hybrid sequencing

Au, K. F., Sebastiano, V., Afshar, P. T., Durruthy, J. D., Lee, L., Williams, B. A., van Bakel, H., Schadt, E. E., Reijo-Pera, R. A., Underwood, J. G., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320101110 · Cited by 341

Long-read sequence assembly of the gorilla genome

Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., Malig, M., Raja, A., Fiddes, I., Hillier, L. W., et al. (2016) · Science · doi:10.1126/science.aae0344 · Cited by 333

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

Liu, Q., Li, F., Yu, G., Wang, D., Xiao, C., & Wang, K. (2019) · Nature Communications · doi:10.1038/s41467-019-10168-2 · Cited by 329

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

Payne, A., Holmes, N., Rakyan, V., & Loose, M. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty841 · Cited by 326

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Quick, J., Ashton, P., Calus, S., Chatt, C., Gossain, S., Hawker, J. I., Nair, S., Neal, K. R., Nye, K., Peters, T. M., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0677-2 · Cited by 317

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

Maio, N. D., Shaw, L. P., Hubbard, A. T. M., George, S. A., Sanderson, N. D., Swann, J., Wick, R. R., AbuOun, M., Stubberfield, E. J., Hoosdally, S., et al. (2019) · Microbial Genomics · doi:10.1099/mgen.0.000294 · Cited by 282

De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal ProcessingPreprint

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A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

Soneson, C., Yao, Y., Bratus-Neuenschwander, A., Patrignani, A., Robinson, M. D., & Hussain, S. (2019) · Nature Communications · doi:10.1038/s41467-019-11272-z · Cited by 277

Defining a personal, allele-specific, and single-molecule long-read transcriptome

Tilgner, H., Grubert, F., Sharon, D., & Snyder, M. P. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400447111 · Cited by 266

Long-read sequencing and de novo assembly of a Chinese genome

Shi, L., Guo, Y., Dong, C., Huddleston, J., Yang, H., Han, X., Fu, A., Li, Q., Li, N., Gong, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms12065 · Cited by 259

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

Ni, P., Huang, N., Zhang, Z., Wang, D., Liang, F., Yu, M., Xiao, C., Luo, F., & Wang, J. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz276 · Cited by 259

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

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Pacific biosciences sequencing technology for genotyping and variation discovery in human data

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Long-read genome sequencing identifies causal structural variation in a Mendelian disease

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Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA

Volden, R., Palmer, T., Byrne, A., Cole, C., Schmitz, R. J., Green, R. E., & Vollmers, C. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1806447115 · Cited by 238

DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics

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Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assemblyPreprint

Wang, O., Chin, R. G., Cheng, X., Wu, M. K. Y., Mao, Q., Tang, J., Sun, Y., Anderson, E., Lam, H. K., Chen, D., et al. (2019) · Genome Research · doi:10.1101/gr.245126.118 · Cited by 229

Deciphering bacterial epigenomes using modern sequencing technologies

Beaulaurier, J., Schadt, E. E., & Fang, G. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0081-3 · Cited by 226

Errors in long-read assemblies can critically affect protein prediction

Watson, M., & Warr, A. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0004-z · Cited by 224

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

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Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

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De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

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Improvements in Genomic Technologies: Application to Crop Genomics

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Human Genome Assembly in 100 MinutesPreprint

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Mycobacterium bovis: From Genotyping to Genome Sequencing

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Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing

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Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events

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Antibodies specific for nucleic acid modifications

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Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brainPreprint

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A sequencer coming of age: De novo genome assembly using MinION reads

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Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster

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Ion Mobility-Mass Spectrometry Reveals That α-Hemolysin from Staphylococcus aureus Simultaneously Forms Hexameric and Heptameric Complexes in Detergent Micelle Solutions

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Hybrid assembly of ultra-long Nanopore reads augmented with 10x-Genomics contigs: Demonstrated with a human genome

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Mapping DNA replication with nanopore sequencingPreprint

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New technologies boost genome quality

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Visualization tools for human structural variations identified by whole-genome sequencing

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Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencingPreprint

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Using dried blood spot samples from a trio for linked-read whole-exome sequencing

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Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communitiesPreprint

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YaHS: yet another Hi-C scaffolding tool

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Nanopore sequencing technology, bioinformatics and applications

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Next-Generation Sequencing Technology: Current Trends and Advancements

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hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data

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A comprehensive evaluation of long read error correction methods

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