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

Author: Grafiati

Published: 8 March 2025

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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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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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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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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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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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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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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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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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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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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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11

Page, Andrew J., and Jacqueline A. Keane. "Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus." PeerJ 6 (July 31, 2018): e5233. http://dx.doi.org/10.7717/peerj.5233.

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Genome sequencing is rapidly being adopted in reference labs and hospitals for bacterial outbreak investigation and diagnostics where time is critical. Seven gene multi-locus sequence typing is a standard tool for broadly classifying samples into sequence types (STs), allowing, in many cases, to rule a sample out of an outbreak, or allowing for general characteristics about a bacterial strain to be inferred. Long-read sequencing technologies, such as from Oxford Nanopore, can produce read data within minutes of an experiment starting, unlike short-read sequencing technologies which require man

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Prodanov, Timofey, and Vikas Bansal. "Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications." Nucleic Acids Research 48, no. 19 (2020): e114-e114. http://dx.doi.org/10.1093/nar/gkaa829.

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Abstract The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read a

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Kumar, Venkatesh, Thomas Vollbrecht, Mark Chernyshev, et al. "Long-read amplicon denoising." Nucleic Acids Research 47, no. 18 (2019): e104-e104. http://dx.doi.org/10.1093/nar/gkz657.

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Abstract Long-read next-generation amplicon sequencing shows promise for studying complete genes or genomes from complex and diverse populations. Current long-read sequencing technologies have challenging error profiles, hindering data processing and incorporation into downstream analyses. Here we consider the problem of how to reconstruct, free of sequencing error, the true sequence variants and their associated frequencies from PacBio reads. Called ‘amplicon denoising’, this problem has been extensively studied for short-read sequencing technologies, but current solutions do not always succe

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Gao, Yahui, Li Ma, and George E. Liu. "Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods." Genes 13, no. 5 (2022): 828. http://dx.doi.org/10.3390/genes13050828.

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Structural variations (SVs), as a great source of genetic variation, are widely distributed in the genome. SVs involve longer genomic sequences and potentially have stronger effects than SNPs, but they are not well captured by short-read sequencing owing to their size and relevance to repeats. Improved characterization of SVs can provide more advanced insight into complex traits. With the availability of long-read sequencing, it has become feasible to uncover the full range of SVs. Here, we sequenced one cattle individual using 10× Genomics (10 × G) linked read, Pacific Biosciences (PacBio) co

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Zhang, Pengfei, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, and Zexiao Yang. "Comparison of De Novo Assembly Strategies for Bacterial Genomes." International Journal of Molecular Sciences 22, no. 14 (2021): 7668. http://dx.doi.org/10.3390/ijms22147668.

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(1) Background: Short-read sequencing allows for the rapid and accurate analysis of the whole bacterial genome but does not usually enable complete genome assembly. Long-read sequencing greatly assists with the resolution of complex bacterial genomes, particularly when combined with short-read Illumina data. However, it is not clear how different assembly strategies affect genomic accuracy, completeness, and protein prediction. (2) Methods: we compare different assembly strategies for Haemophilus parasuis, which causes Glässer’s disease, characterized by fibrinous polyserositis and arthritis,

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Yu, Xiaoling, Wenqian Jiang, Xinhui Huang, Jun Lin, Hanhui Ye, and Baorong Liu. "rRNA Analysis Based on Long-Read High-Throughput Sequencing Reveals a More Accurate Diagnostic for the Bacterial Infection of Ascites." BioMed Research International 2021 (November 17, 2021): 1–8. http://dx.doi.org/10.1155/2021/6287280.

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Traditional pathogenic diagnosis presents defects such as a low positivity rate, inability to identify uncultured microorganisms, and time-consuming nature. Clinical metagenomics next-generation sequencing can be used to detect any pathogen, compensating for the shortcomings of traditional pathogenic diagnosis. We report third-generation long-read sequencing results and second-generation short-read sequencing results for ascitic fluid from a patient with liver ascites and compared the two types of sequencing results with the results of traditional clinical microbial culture. The distribution o

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Cechova, Monika. "Probably Correct: Rescuing Repeats with Short and Long Reads." Genes 12, no. 1 (2020): 48. http://dx.doi.org/10.3390/genes12010048.

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Ever since the introduction of high-throughput sequencing following the human genome project, assembling short reads into a reference of sufficient quality posed a significant problem as a large portion of the human genome—estimated 50–69%—is repetitive. As a result, a sizable proportion of sequencing reads is multi-mapping, i.e., without a unique placement in the genome. The two key parameters for whether or not a read is multi-mapping are the read length and genome complexity. Long reads are now able to span difficult, heterochromatic regions, including full centromeres, and characterize chr

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Kainth, Amoldeep S., Gabriela A. Haddad, Johnathon M. Hall, and Alexander J. Ruthenburg. "Merging short and stranded long reads improves transcript assembly." PLOS Computational Biology 19, no. 10 (2023): e1011576. http://dx.doi.org/10.1371/journal.pcbi.1011576.

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Long-read RNA sequencing has arisen as a counterpart to short-read sequencing, with the potential to capture full-length isoforms, albeit at the cost of lower depth. Yet this potential is not fully realized due to inherent limitations of current long-read assembly methods and underdeveloped approaches to integrate short-read data. Here, we critically compare the existing methods and develop a new integrative approach to characterize a particularly challenging pool of low-abundance long noncoding RNA (lncRNA) transcripts from short- and long-read sequencing in two distinct cell lines. Our analy

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Zablocki, Olivier, Michelle Michelsen, Marie Burris, et al. "VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature." PeerJ 9 (March 30, 2021): e11088. http://dx.doi.org/10.7717/peerj.11088.

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Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressur

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Lecompte, Lolita, Pierre Peterlongo, Dominique Lavenier, and Claire Lemaitre. "SVJedi: genotyping structural variations with long reads." Bioinformatics 36, no. 17 (2020): 4568–75. http://dx.doi.org/10.1093/bioinformatics/btaa527.

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Abstract Motivation Studies on structural variants (SVs) are expanding rapidly. As a result, and thanks to third generation sequencing technologies, the number of discovered SVs is increasing, especially in the human genome. At the same time, for several applications such as clinical diagnoses, it is important to genotype newly sequenced individuals on well-defined and characterized SVs. Whereas several SV genotypers have been developed for short read data, there is a lack of such dedicated tool to assess whether known SVs are present or not in a new long read sequenced sample, such as the one

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Wommack, K. Eric, Jaysheel Bhavsar, and Jacques Ravel. "Metagenomics: Read Length Matters." Applied and Environmental Microbiology 74, no. 5 (2008): 1453–63. http://dx.doi.org/10.1128/aem.02181-07.

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ABSTRACT Obtaining an unbiased view of the phylogenetic composition and functional diversity within a microbial community is one central objective of metagenomic analysis. New technologies, such as 454 pyrosequencing, have dramatically reduced sequencing costs, to a level where metagenomic analysis may become a viable alternative to more-focused assessments of the phylogenetic (e.g., 16S rRNA genes) and functional diversity of microbial communities. To determine whether the short (∼100 to 200 bp) sequence reads obtained from pyrosequencing are appropriate for the phylogenetic and functional ch

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Sierra, Roberto, Mélanie Roch, Milo Moraz, et al. "Contributions of Long-Read Sequencing for the Detection of Antimicrobial Resistance." Pathogens 13, no. 9 (2024): 730. http://dx.doi.org/10.3390/pathogens13090730.

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Background. In the context of increasing antimicrobial resistance (AMR), whole-genome sequencing (WGS) of bacteria is considered a highly accurate and comprehensive surveillance method for detecting and tracking the spread of resistant pathogens. Two primary sequencing technologies exist: short-read sequencing (50–300 base pairs) and long-read sequencing (thousands of base pairs). The former, based on Illumina sequencing platforms (ISPs), provides extensive coverage and high accuracy for detecting single nucleotide polymorphisms (SNPs) and small insertions/deletions, but is limited by its read

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Wei, Po-Li, Ching-Sheng Hung, Yi-Wei Kao, et al. "Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform." International Journal of Molecular Sciences 21, no. 19 (2020): 7110. http://dx.doi.org/10.3390/ijms21197110.

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Accurate and rapid identification of microbiotic communities using 16S ribosomal (r)RNA sequencing is a critical task for expanding medical and clinical applications. Next-generation sequencing (NGS) is widely considered a practical approach for direct application to communities without the need for in vitro culturing. In this report, a comparative evaluation of short-read (Illumina) and long-read (Oxford Nanopore Technologies (ONT)) platforms toward 16S rRNA sequencing with the same batch of total genomic DNA extracted from fecal samples is presented. Different 16S gene regions were amplified

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Holmqvist, Isak, Alan Bäckerholm, Yarong Tian, Guojiang Xie, Kaisa Thorell, and Ka-Wei Tang. "FLAME: long-read bioinformatics tool for comprehensive spliceome characterization." RNA 27, no. 10 (2021): 1127–39. http://dx.doi.org/10.1261/rna.078800.121.

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Comprehensive characterization of differentially spliced RNA transcripts with nanopore sequencing is limited by bioinformatics tools that are reliant on existing annotations. We have developed FLAME, a bioinformatics pipeline for alternative splicing analysis of gene-specific or transcriptome-wide long-read sequencing data. FLAME is a Python-based tool aimed at providing comprehensible quantification of full-length splice variants, reliable de novo recognition of splice sites and exons, and representation of consecutive exon connectivity in the form of a weighted adjacency matrix. Notably, thi

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Gouil, Quentin, and Andrew Keniry. "Latest techniques to study DNA methylation." Essays in Biochemistry 63, no. 6 (2019): 639–48. http://dx.doi.org/10.1042/ebc20190027.

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Abstract Bisulfite sequencing is a powerful technique to detect 5-methylcytosine in DNA that has immensely contributed to our understanding of epigenetic regulation in plants and animals. Meanwhile, research on other base modifications, including 6-methyladenine and 4-methylcytosine that are frequent in prokaryotes, has been impeded by the lack of a comparable technique. Bisulfite sequencing also suffers from a number of drawbacks that are difficult to surmount, among which DNA degradation, lack of specificity, or short reads with low sequence diversity. In this review, we explore the recent r

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Chaux, Frédéric, Nicolas Agier, Stephan Eberhard, and Zhou Xu. "Extraction and selection of high-molecular-weight DNA for long-read sequencing from Chlamydomonas reinhardtii." PLOS ONE 19, no. 2 (2024): e0297014. http://dx.doi.org/10.1371/journal.pone.0297014.

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Recent advances in long-read sequencing technologies have enabled the complete assembly of eukaryotic genomes from telomere to telomere by allowing repeated regions to be fully sequenced and assembled, thus filling the gaps left by previous short-read sequencing methods. Furthermore, long-read sequencing can also help characterizing structural variants, with applications in the fields of genome evolution or cancer genomics. For many organisms, the main bottleneck to sequence long reads remains the lack of robust methods to obtain high-molecular-weight (HMW) DNA. For this purpose, we developed

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Su, Yun, Liyuan Fan, Changhe Shi, et al. "Deciphering Neurodegenerative Diseases Using Long-Read Sequencing." Neurology 97, no. 9 (2021): 423–33. http://dx.doi.org/10.1212/wnl.0000000000012466.

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Neurodegenerative diseases exhibit chronic progressive lesions in the central and peripheral nervous systems with unclear causes. The search for pathogenic mutations in human neurodegenerative diseases has benefited from massively parallel short-read sequencers. However, genomic regions, including repetitive elements, especially with high/low GC content, are far beyond the capability of conventional approaches. Recently, long-read single-molecule DNA sequencing technologies have emerged and enabled researchers to study genomes, transcriptomes, and metagenomes at unprecedented resolutions. The

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Heller, David, and Martin Vingron. "SVIM: structural variant identification using mapped long reads." Bioinformatics 35, no. 17 (2019): 2907–15. http://dx.doi.org/10.1093/bioinformatics/btz041.

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Abstract Motivation Structural variants are defined as genomic variants larger than 50 bp. They have been shown to affect more bases in any given genome than single-nucleotide polymorphisms or small insertions and deletions. Additionally, they have great impact on human phenotype and diversity and have been linked to numerous diseases. Due to their size and association with repeats, they are difficult to detect by shotgun sequencing, especially when based on short reads. Long read, single-molecule sequencing technologies like those offered by Pacific Biosciences or Oxford Nanopore Technologies

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Pushel, Irina, Lisa A. Lansdon, Byunggil Yoo, et al. "Short- and Long-Read RNA Sequencing Improve Molecular Profiling of Pediatric T-Cell Acute Lymphoblastic Leukemia." Blood 144, Supplement 1 (2024): 5921. https://doi.org/10.1182/blood-2024-208984.

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Acute lymphoblastic leukemia (ALL) is one of the most common pediatric cancers, accounting for approximately 1/3 of childhood cancer diagnoses. Of these patients, ~15% are diagnosed with T-cell ALL (T-ALL). Pediatric T-ALL is less well-characterized and has a worse prognosis than its B-cell counterpart, particularly after relapse. Although many genetic drivers for pediatric T-ALL have been characterized, this information does not currently inform treatment selection for patients. By integrating transcriptional profiling data with genomic findings from molecular and cytogenetic assays, we aim t

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Broseus, Lucile, Aubin Thomas, Andrew J. Oldfield, Dany Severac, Emeric Dubois, and William Ritchie. "TALC: Transcript-level Aware Long-read Correction." Bioinformatics 36, no. 20 (2020): 5000–5006. http://dx.doi.org/10.1093/bioinformatics/btaa634.

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Abstract Motivation Long-read sequencing technologies are invaluable for determining complex RNA transcript architectures but are error-prone. Numerous ‘hybrid correction’ algorithms have been developed for genomic data that correct long reads by exploiting the accuracy and depth of short reads sequenced from the same sample. These algorithms are not suited for correcting more complex transcriptome sequencing data. Results We have created a novel reference-free algorithm called Transcript-level Aware Long-Read Correction (TALC) which models changes in RNA expression and isoform representation

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Wick, Ryan R., and Kathryn E. Holt. "Benchmarking of long-read assemblers for prokaryote whole genome sequencing." F1000Research 8 (December 23, 2019): 2138. http://dx.doi.org/10.12688/f1000research.21782.1.

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Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of six long-read assemblers (Canu, Flye, Mi

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Wick, Ryan R., and Kathryn E. Holt. "Benchmarking of long-read assemblers for prokaryote whole genome sequencing." F1000Research 8 (April 22, 2020): 2138. http://dx.doi.org/10.12688/f1000research.21782.2.

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Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of seven long-read assemblers (Canu, Flye,

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Thibodeau, My Linh, Kieran O’Neill, Katherine Dixon, et al. "Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing." Genetics in Medicine 22, no. 11 (2020): 1892–97. http://dx.doi.org/10.1038/s41436-020-0880-8.

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Abstract Purpose Structural variants (SVs) may be an underestimated cause of hereditary cancer syndromes given the current limitations of short-read next-generation sequencing. Here we investigated the utility of long-read sequencing in resolving germline SVs in cancer susceptibility genes detected through short-read genome sequencing. Methods Known or suspected deleterious germline SVs were identified using Illumina genome sequencing across a cohort of 669 advanced cancer patients with paired tumor genome and transcriptome sequencing. Candidate SVs were subsequently assessed by Oxford Nanopor

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Anantharam, Raghavendran, Dylan Duchen, Andrea L. Cox, et al. "Long-Read Nanopore-Based Sequencing of Anelloviruses." Viruses 16, no. 5 (2024): 723. http://dx.doi.org/10.3390/v16050723.

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Routinely used metagenomic next-generation sequencing (mNGS) techniques often fail to detect low-level viremia (<104 copies/mL) and appear biased towards viruses with linear genomes. These limitations hinder the capacity to comprehensively characterize viral infections, such as those attributed to the Anelloviridae family. These near ubiquitous non-pathogenic components of the human virome have circular single-stranded DNA genomes that vary in size from 2.0 to 3.9 kb and exhibit high genetic diversity. Hence, species identification using short reads can be challenging. Here, we introduce a

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Das, Arghya Kusum, Sayan Goswami, Kisung Lee, and Seung-Jong Park. "A hybrid and scalable error correction algorithm for indel and substitution errors of long reads." BMC Genomics 20, S11 (2019). http://dx.doi.org/10.1186/s12864-019-6286-9.

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Abstract Background Long-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly. However, the computation of the long sequencing reads is challenged by their higher error rates (e.g., 13% vs. 1%) and higher cost ($0.3 vs. $0.03 per Mbp) compared to the short reads. Methods In this paper, we present a new hybrid error correction tool, called ParLECH (Parallel Long-read Error Correction using Hybrid methodology). The error correction algorithm of ParLECH is distributed in nature and efficiently utilizes

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Babarinde, Isaac Adeyemi, and Andrew Paul Hutchins. "The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome." BMC Genomics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12864-022-08717-z.

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AbstractInvestigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts. This heterogeneity in assembled transcript sets might be partially explained by sequencing depth. Here, we used real and simulated short-read sequencing data as well as long-read data to systematically investigate the impact of sequencing depths on the accuracy of assembled transcripts. We assembled and analyzed transcripts from

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Kovaka, Sam, Aleksey V. Zimin, Geo M. Pertea, Roham Razaghi, Steven L. Salzberg, and Mihaela Pertea. "Transcriptome assembly from long-read RNA-seq alignments with StringTie2." Genome Biology 20, no. 1 (2019). http://dx.doi.org/10.1186/s13059-019-1910-1.

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AbstractRNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads. StringTie2 includes new methods to handle the high error rate of long reads and offers the ability to work with full-length super-reads assembled from short reads, which further improves the quality of short-read assemblies. StringTie2 is more accurate

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Yang, Chao, Zhenmiao Zhang, Yufen Huang, et al. "LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome." GigaScience 13 (2024). http://dx.doi.org/10.1093/gigascience/giae028.

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Abstract Background Linked-read sequencing technologies generate high-base quality short reads that contain extrapolative information on long-range DNA connectedness. These advantages of linked-read technologies are well known and have been demonstrated in many human genomic and metagenomic studies. However, existing linked-read analysis pipelines (e.g., Long Ranger) were primarily developed to process sequencing data from the human genome and are not suited for analyzing metagenomic sequencing data. Moreover, linked-read analysis pipelines are typically limited to 1 specific sequencing platfo

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Kallenborn, Felix, and Bertil Schmidt. "CAREx: context-aware read extension of paired-end sequencing data." BMC Bioinformatics 25, no. 1 (2024). http://dx.doi.org/10.1186/s12859-024-05802-w.

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Abstract Background Commonly used next generation sequencing machines typically produce large amounts of short reads of a few hundred base-pairs in length. However, many downstream applications would generally benefit from longer reads. Results We present CAREx—an algorithm for the generation of pseudo-long reads from paired-end short-read Illumina data based on the concept of repeatedly computing multiple-sequence-alignments to extend a read until its partner is found. Our performance evaluation on both simulated data and real data shows that CAREx is able to connect significantly more read p

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Zee, Alexander, Dori Zhi Qian Deng, Matthew Adams, et al. "Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2." Genome Research, November 9, 2022, gr.277031.122. http://dx.doi.org/10.1101/gr.277031.122.

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High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays exist today to take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short-read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities, and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-

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Meleshko, Dmitry, Andrey D. Prjbelski, Mikhail Raiko, Alexandru I. Tomescu, Hagen Tilgner, and Iman Hajirasouliha. "cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data." Bioinformatics, January 23, 2024. http://dx.doi.org/10.1093/bioinformatics/btad781.

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Abstract Motivation Recent advancements in long-read RNA sequencing have enabled the examination of full-length isoforms, previously uncaptured by short-read sequencing methods. An alternative powerful method for studying isoforms is through the use of barcoded short-read RNA reads, for which a barcode indicates whether two short-reads arise from the same molecule or not. Such techniques included the 10x Genomics linked-read based SParse Isoform Sequencing (SPIso-seq), as well as Loop-Seq, or Tell-Seq. Some applications, such as novel-isoform discovery, require very high coverage. Obtaining hi

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Karaoglanoglu, Fatih, Cedric Chauve, and Faraz Hach. "Genion, an accurate tool to detect gene fusion from long transcriptomics reads." BMC Genomics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12864-022-08339-5.

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Abstract Background The advent of next-generation sequencing technologies empowered a wide variety of transcriptomics studies. A widely studied topic is gene fusion which is observed in many cancer types and suspected of having oncogenic properties. Gene fusions are the result of structural genomic events that bring two genes closely located and result in a fused transcript. This is different from fusion transcripts created during or after the transcription process. These chimeric transcripts are also known as read-through and trans-splicing transcripts. Gene fusion discovery with short reads

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Commichaux, Seth, Kiran Javkar, Padmini Ramachandran, et al. "Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads." BMC Genomics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12864-021-07702-2.

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Abstract Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower

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Liu, Silvia, Caroline Obert, Yan-Ping Yu, et al. "Utility analyses of AVITI sequencing chemistry." BMC Genomics 25, no. 1 (2024). http://dx.doi.org/10.1186/s12864-024-10686-4.

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Abstract Background DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Results Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences’ AVITI and Illumina’s NextSeq 550 chemistries

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De Coster, Wouter, Mojca Strazisar, and Peter De Rijk. "Critical length in long-read resequencing." NAR Genomics and Bioinformatics 2, no. 1 (2020). http://dx.doi.org/10.1093/nargab/lqz027.

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Abstract Long-read sequencing has substantial advantages for structural variant discovery and phasing of variants compared to short-read technologies, but the required and optimal read length has not been assessed. In this work, we used long reads simulated from human genomes and evaluated structural variant discovery and variant phasing using current best practice bioinformatics methods. We determined that optimal discovery of structural variants from human genomes can be obtained with reads of minimally 20 kb. Haplotyping variants across genes only reaches its optimum from reads of 100 kb. T

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Neubert, Kerstin, Eric Zuchantke, Robert Maximilian Leidenfrost, et al. "Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures." BMC Genomics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12864-021-08115-x.

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Abstract Background We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation “short-read” and third-generation “long-read” sequencing methods. Results We focused on short-read assemblers, hybrid assemblers, and analysis o

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Gehrig, Jeanette L., Daniel M. Portik, Mark D. Driscoll, et al. "Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data." Microbial Genomics 8, no. 3 (2022). http://dx.doi.org/10.1099/mgen.0.000794.

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A long-standing challenge in human microbiome research is achieving the taxonomic and functional resolution needed to generate testable hypotheses about the gut microbiota’s impact on health and disease. With a growing number of live microbial interventions in clinical development, this challenge is renewed by a need to understand the pharmacokinetics and pharmacodynamics of therapeutic candidates. While short-read sequencing of the bacterial 16S rRNA gene has been the standard for microbiota profiling, recent improvements in the fidelity of long-read sequencing underscores the need for a re-e

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Fang, Li, Charlly Kao, Michael V. Gonzalez, et al. "LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data." Nature Communications 10, no. 1 (2019). http://dx.doi.org/10.1038/s41467-019-13397-7.

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AbstractLinked-read sequencing provides long-range information on short-read sequencing data by barcoding reads originating from the same DNA molecule, and can improve detection and breakpoint identification for structural variants (SVs). Here we present LinkedSV for SV detection on linked-read sequencing data. LinkedSV considers barcode overlapping and enriched fragment endpoints as signals to detect large SVs, while it leverages read depth, paired-end signals and local assembly to detect small SVs. Benchmarking studies demonstrate that LinkedSV outperforms existing tools, especially on exome

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Mak, Lauren, Dmitry Meleshko, David C. Danko, et al. "Ariadne: synthetic long read deconvolution using assembly graphs." Genome Biology 24, no. 1 (2023). http://dx.doi.org/10.1186/s13059-023-03033-5.

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AbstractSynthetic long read sequencing techniques such as UST’s TELL-Seq and Loop Genomics’ LoopSeq combine 3$$'$$ ′ barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. However, the lack of a 1:1 correspondence between a long fragment and a 3$$'$$ ′ unique molecular identifier confounds the assignment of linkage between short reads. We introduce Ariadne, a novel assembly graph-based synthetic long read deconvolution algorithm, that can be used to extract single-species read-clouds from synthetic long read dat

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Portik, Daniel M., C. Titus Brown, and N. Tessa Pierce-Ward. "Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets." BMC Bioinformatics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12859-022-05103-0.

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Abstract Background Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic classification and profiling. The development of long-read specific tools for taxonomic classification is accelerating, yet there is a lack of information regarding their relative performance. Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to

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