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Relevant bibliographies by topics / Short read and long read sequencing

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Journal articles

Academic literature on the topic 'Short read and long read sequencing'

Author: Grafiati

Published: 8 March 2025

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Journal articles on the topic "Short read and long read sequencing"

1

Shumate, Alaina, Brandon Wong, Geo Pertea, and Mihaela Pertea. "Improved transcriptome assembly using a hybrid of long and short reads with StringTie." PLOS Computational Biology 18, no. 6 (2022): e1009730. http://dx.doi.org/10.1371/journal.pcbi.1009730.

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Short-read RNA sequencing and long-read RNA sequencing each have their strengths and weaknesses for transcriptome assembly. While short reads are highly accurate, they are rarely able to span multiple exons. Long-read technology can capture full-length transcripts, but its relatively high error rate often leads to mis-identified splice sites. Here we present a new release of StringTie that performs hybrid-read assembly. By taking advantage of the strengths of both long and short reads, hybrid-read assembly with StringTie is more accurate than long-read only or short-read only assembly, and on

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2

Stapleton, James A., Jeongwoon Kim, John P. Hamilton, et al. "Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing." PLOS ONE 11, no. 1 (2016): e0147229. http://dx.doi.org/10.1371/journal.pone.0147229.

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3

Nguyen, Son Hoang, Minh Duc Cao, and Lachlan J. M. Coin. "Real-time resolution of short-read assembly graph using ONT long reads." PLOS Computational Biology 17, no. 1 (2021): e1008586. http://dx.doi.org/10.1371/journal.pcbi.1008586.

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A streaming assembly pipeline utilising real-time Oxford Nanopore Technology (ONT) sequencing data is important for saving sequencing resources and reducing time-to-result. A previous approach implemented in npScarf provided an efficient streaming algorithm for hybrid assembly but was relatively prone to mis-assemblies compared to other graph-based methods. Here we present npGraph, a streaming hybrid assembly tool using the assembly graph instead of the separated pre-assembly contigs. It is able to produce more complete genome assembly by resolving the path finding problem on the assembly grap

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4

Greenman, Noah, Sayf Al-Deen Hassouneh, Latifa S. Abdelli, Catherine Johnston, and Taj Azarian. "Improving Bacterial Metagenomic Research through Long-Read Sequencing." Microorganisms 12, no. 5 (2024): 935. http://dx.doi.org/10.3390/microorganisms12050935.

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Metagenomic sequencing analysis is central to investigating microbial communities in clinical and environmental studies. Short-read sequencing remains the primary approach for metagenomic research; however, long-read sequencing may offer advantages of improved metagenomic assembly and resolved taxonomic identification. To compare the relative performance for metagenomic studies, we simulated short- and long-read datasets using increasingly complex metagenomes comprising 10, 20, and 50 microbial taxa. Additionally, we used an empirical dataset of paired short- and long-read data generated from

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5

Craddock, Hillary A., Yair Motro, Bar Zilberman, Boris Khalfin, Svetlana Bardenstein, and Jacob Moran-Gilad. "Long-Read Sequencing and Hybrid Assembly for Genomic Analysis of Clinical Brucella melitensis Isolates." Microorganisms 10, no. 3 (2022): 619. http://dx.doi.org/10.3390/microorganisms10030619.

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Brucella melitensis is a key etiological agent of brucellosis and has been increasingly subject to characterization using sequencing methodologies. This study aimed to investigate and compare short-read, long-read, and hybrid assemblies of B. melitensis. Eighteen B. melitensis isolates from Southern Israel were sequenced using Illumina and the Oxford Nanopore (ONP) MinION, and hybrid assemblies were generated with ONP long reads scaffolded on Illumina short reads. Short reads were assembled with INNUca with SPADes, long reads and hybrid with dragonflye. Abricate with the virulence factor datab

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6

Botton, Mariana R., Yao Yang, Erick R. Scott, Robert J. Desnick, and Stuart A. Scott. "Phased Haplotype Resolution of the SLC6A4 Promoter Using Long-Read Single Molecule Real-Time (SMRT) Sequencing." Genes 11, no. 11 (2020): 1333. http://dx.doi.org/10.3390/genes11111333.

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The SLC6A4 gene has been implicated in psychiatric disorder susceptibility and antidepressant response variability. The SLC6A4 promoter is defined by a variable number of homologous 20–24 bp repeats (5-HTTLPR), and long (L) and short (S) alleles are associated with higher and lower expression, respectively. However, this insertion/deletion variant is most informative when considered as a haplotype with the rs25531 and rs25532 variants. Therefore, we developed a long-read single molecule real-time (SMRT) sequencing method to interrogate the SLC6A4 promoter region. A total of 120 samples were su

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7

Volden, Roger, Theron Palmer, Ashley Byrne, et al. "Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA." Proceedings of the National Academy of Sciences 115, no. 39 (2018): 9726–31. http://dx.doi.org/10.1073/pnas.1806447115.

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High-throughput short-read sequencing has revolutionized how transcriptomes are quantified and annotated. However, while Illumina short-read sequencers can be used to analyze entire transcriptomes down to the level of individual splicing events with great accuracy, they fall short of analyzing how these individual events are combined into complete RNA transcript isoforms. Because of this shortfall, long-distance information is required to complement short-read sequencing to analyze transcriptomes on the level of full-length RNA transcript isoforms. While long-read sequencing technology can pro

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8

Iyer, Shruti V., Sara Goodwin, and William Richard McCombie. "Leveraging the power of long reads for targeted sequencing." Genome Research 34, no. 11 (2024): 1701–18. http://dx.doi.org/10.1101/gr.279168.124.

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Long-read sequencing technologies have improved the contiguity and, as a result, the quality of genome assemblies by generating reads long enough to span and resolve complex or repetitive regions of the genome. Several groups have shown the power of long reads in detecting thousands of genomic and epigenomic features that were previously missed by short-read sequencing approaches. While these studies demonstrate how long reads can help resolve repetitive and complex regions of the genome, they also highlight the throughput and coverage requirements needed to accurately resolve variant alleles

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9

Wick, Ryan R., Louise M. Judd, and Kathryn E. Holt. "Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing." PLOS Computational Biology 19, no. 3 (2023): e1010905. http://dx.doi.org/10.1371/journal.pcbi.1010905.

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A perfect bacterial genome assembly is one where the assembled sequence is an exact match for the organism’s genome—each replicon sequence is complete and contains no errors. While this has been difficult to achieve in the past, improvements in long-read sequencing, assemblers, and polishers have brought perfect assemblies within reach. Here, we describe our recommended approach for assembling a bacterial genome to perfection using a combination of Oxford Nanopore Technologies long reads and Illumina short reads: Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read p

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10

Eisenstein, Michael. "Startups use short-read data to expand long-read sequencing market." Nature Biotechnology 33, no. 5 (2015): 433–35. http://dx.doi.org/10.1038/nbt0515-433.

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