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Journal articles on the topic 'High-throughput sequencing of the genome'

Author: Grafiati
Published: 7 June 2025
Last updated: 2 August 2025

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1

Montmayeur, Anna M., Terry Fei Fan Ng, Alexander Schmidt, et al. "High-Throughput Next-Generation Sequencing of Polioviruses." Journal of Clinical Microbiology 55, no. 2 (2016): 606–15. http://dx.doi.org/10.1128/jcm.02121-16.

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ABSTRACTThe poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random reverse transcript
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2

YE, Bing-gang, De-peng WANG, Jing-xiang LI, Yan ZHOU, and Xiao-ming WU. "Phase emendation of high-throughput genome sequencing." Journal of Computer Applications 30, no. 4 (2010): 1114–16. http://dx.doi.org/10.3724/sp.j.1087.2010.01114.

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3

Parrish, Nathaniel, Benjamin Sudakov, and Eleazar Eskin. "Genome reassembly with high-throughput sequencing data." BMC Genomics 14, Suppl 1 (2013): S8. http://dx.doi.org/10.1186/1471-2164-14-s1-s8.

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4

Kunz, Manfred, Michael Dannemann, and Janet Kelso. "High-throughput sequencing of the melanoma genome." Experimental Dermatology 22, no. 1 (2012): 10–17. http://dx.doi.org/10.1111/exd.12054.

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5

Huang, Yong, Meiqi Shang, Tingting Liu, and Kejian Wang. "High-throughput methods for genome editing: the more the better." Plant Physiology 188, no. 4 (2022): 1731–45. http://dx.doi.org/10.1093/plphys/kiac017.

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Abstract During the last decade, targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) technologies, have permitted efficient targeting of genomes, thereby modifying these genomes to offer tremendous opportunities for deciphering gene function and engineering beneficial traits in many biological systems. As a powerful genome-editing tool, the CRISPR/Cas systems, combined with the development of next-generation sequencing and many other high-throughput techniques, have thus been quickly developed into a
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6

Harvey, N. R., C. L. Albury, S. Stuart, et al. "Ion torrent high throughput mitochondrial genome sequencing (HTMGS)." PLOS ONE 14, no. 11 (2019): e0224847. http://dx.doi.org/10.1371/journal.pone.0224847.

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7

Dalca, A. V., and M. Brudno. "Genome variation discovery with high-throughput sequencing data." Briefings in Bioinformatics 11, no. 1 (2010): 3–14. http://dx.doi.org/10.1093/bib/bbp058.

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8

Li, Shasha, Hang Fan, Xiaoping An, et al. "Scrutinizing Virus Genome Termini by High-Throughput Sequencing." PLoS ONE 9, no. 1 (2014): e85806. http://dx.doi.org/10.1371/journal.pone.0085806.

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9

Fiume, M., V. Williams, A. Brook, and M. Brudno. "Savant: genome browser for high-throughput sequencing data." Bioinformatics 26, no. 16 (2010): 1938–44. http://dx.doi.org/10.1093/bioinformatics/btq332.

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10

Gurgul, Artur, Igor Jasielczuk, Tomasz Szmatoła, et al. "Application of Nanopore Sequencing for High Throughput Genotyping in Horses." Animals 13, no. 13 (2023): 2227. http://dx.doi.org/10.3390/ani13132227.

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Nanopore sequencing is a third-generation biopolymer sequencing technique that relies on monitoring the changes in an electrical current that occur as nucleic acids are passed through a protein nanopore. Increasing quality of reads generated by nanopore sequencing systems encourages their application in genome-wide polymorphism detection and genotyping. In this study, we employed nanopore sequencing to identify genome-wide polymorphisms in the horse genome. To reduce the size and complexity of genome fragments for sequencing in a simple and cost-efficient manner, we amplified random DNA fragme
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11

Kim, Dae-Won, Seong-Hyeuk Nam, Ryong Nam Kim, Sang-Haeng Choi, and Hong-Seog Park. "Whole human exome capture for high-throughput sequencing." Genome 53, no. 7 (2010): 568–74. http://dx.doi.org/10.1139/g10-025.

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We captured the whole human exome by hybridization using synthesized oligonucleotides, based on a high-density microarray design, and we sequenced those captured human exons using high-throughput sequencing on a Genome Sequencer FLX instrument. Of the uniquely mapped reads, 71% fell within target regions, and these corresponded to coverage of 94% of human genes, 87% of exons, and 70% of the total base-pair length of the CCDS set. Our study provides strong evidence for the practical usefulness of this method on a genome-wide scale, showing the resequenced whole human exome database with 501 mic
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12

Ben Khedher, Mariem, Kais Ghedira, Jean-Marc Rolain, Raymond Ruimy, and Olivier Croce. "Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies." International Journal of Molecular Sciences 23, no. 3 (2022): 1395. http://dx.doi.org/10.3390/ijms23031395.

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Over the past 25 years, the powerful combination of genome sequencing and bioinformatics analysis has played a crucial role in interpreting information encoded in bacterial genomes. High-throughput sequencing technologies have paved the way towards understanding an increasingly wide range of biological questions. This revolution has enabled advances in areas ranging from genome composition to how proteins interact with nucleic acids. This has created unprecedented opportunities through the integration of genomic data into clinics for the diagnosis of genetic traits associated with disease. Sin
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13

Zhang, Shaokang, Yanlong Yin, Marcus B. Jones, et al. "Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data." Journal of Clinical Microbiology 53, no. 5 (2015): 1685–92. http://dx.doi.org/10.1128/jcm.00323-15.

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14

Wang, Jiyue, Denghong Shi, Yu Bai, and Yan Liu. "High-throughput sequencing uncover Ficus tikoua Bur. chloroplast genome." Journal of Plant Biochemistry and Biotechnology 29, no. 2 (2019): 171–82. http://dx.doi.org/10.1007/s13562-019-00537-9.

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15

Rihtman, Branko, Sean Meaden, Martha R. J. Clokie, Britt Koskella, and Andrew D. Millard. "Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes." PeerJ 4 (June 1, 2016): e2055. http://dx.doi.org/10.7717/peerj.2055.

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Bacteriophages are the most abundant biological entities on the planet, playing crucial roles in the shaping of bacterial populations. Phages have smaller genomes than their bacterial hosts, yet there are currently fewer fully sequenced phage than bacterial genomes. We assessed the suitability of Illumina technology for high-throughput sequencing and subsequent assembly of phage genomes. In silico datasets reveal that 30× coverage is sufficient to correctly assemble the complete genome of ˜98.5% of known phages, with experimental data confirming that the majority of phage genomes can be assemb
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16

Rice, Edward S., and Richard E. Green. "New Approaches for Genome Assembly and Scaffolding." Annual Review of Animal Biosciences 7, no. 1 (2019): 17–40. http://dx.doi.org/10.1146/annurev-animal-020518-115344.

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Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome assemblies from high-throughput, short-read sequencing, however, are often not as contiguous as the first generation of genome assemblies. Whereas early genome assembly projects were often aided by clone maps or other mapping data, many current assembly projects forego these scaffolding data and only assemble genomes into smaller segments. Recently, new technologies have been invented that allow chromosome-scale assembly at a lower cost and faster speed than traditional methods.
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17

Nakagawa, Hidewaki. "Prostate cancer genomics by high-throughput technologies: genome-wide association study and sequencing analysis." Endocrine-Related Cancer 20, no. 4 (2013): R171—R181. http://dx.doi.org/10.1530/erc-13-0113.

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Prostate cancer (PC) is the most common malignancy in males. It is evident that genetic factors at both germline and somatic levels play critical roles in prostate carcinogenesis. Recently, genome-wide association studies (GWAS) by high-throughput genotyping technology have identified more than 70 germline variants of various genes or chromosome loci that are significantly associated with PC susceptibility. They include multiple 8q24 loci, prostate-specific genes, and metabolism-related genes. Somatic alterations in PC genomes have been explored by high-throughput sequencing technologies such
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18

Longtin, Amy, Marina M. Watowich, Baptiste Sadoughi, et al. "Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing." PLOS Genetics 21, no. 5 (2025): e1011667. https://doi.org/10.1371/journal.pgen.1011667.

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Characterizing DNA methylation patterns is important for addressing key questions in evolutionary biology, development, geroscience, and medical genomics. While costs are decreasing, whole-genome DNA methylation profiling remains prohibitively expensive for most population-scale studies, creating a need for cost-effective, reduced representation approaches (i.e., assays that rely on microarrays, enzyme digests, or sequence capture to target a subset of the genome). Most common whole genome and reduced representation techniques rely on bisulfite conversion, which can damage DNA resulting in DNA
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19

Kechin, Andrey, Viktoria Borobova, Ulyana Boyarskikh, Evgeniy Khrapov, Sergey Subbotin, and Maxim Filipenko. "NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions." PLOS Computational Biology 16, no. 12 (2020): e1008468. http://dx.doi.org/10.1371/journal.pcbi.1008468.

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Multiplex polymerase chain reaction (PCR) has multiple applications in molecular biology, including developing new targeted next-generation sequencing (NGS) panels. We present NGS-PrimerPlex, an efficient and versatile command-line application that designs primers for different refined types of amplicon-based genome target enrichment. It supports nested and anchored multiplex PCR, redistribution among multiplex reactions of primers constructed earlier, and extension of existing NGS-panels. The primer design process takes into consideration the formation of secondary structures, non-target ampl
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20

Bester, Rachelle, Glynnis Cook, and Hans J. Maree. "Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing." Viruses 13, no. 2 (2021): 168. http://dx.doi.org/10.3390/v13020168.

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The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was e
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21

Ong'era, Edidah M., Khadija Said Mohammed, Timothy O. Makori, et al. "High-throughput sequencing approaches applied to SARS-CoV-2." Wellcome Open Research 8 (March 31, 2023): 150. http://dx.doi.org/10.12688/wellcomeopenres.18701.1.

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High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe a
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22

Lyons, Elizabeth A., Melissa K. Scheible, Kimberly Sturk-Andreaggi, Jodi A. Irwin, and Rebecca S. Just. "A high-throughput Sanger strategy for human mitochondrial genome sequencing." BMC Genomics 14, no. 1 (2013): 881. http://dx.doi.org/10.1186/1471-2164-14-881.

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23

Mardis, E. R. "Engineering in genomics. Technical improvements in high throughput genome sequencing." IEEE Engineering in Medicine and Biology Magazine 14, no. 6 (1995): 794–97. http://dx.doi.org/10.1109/51.473281.

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24

A. Pater, Adrian, Michael S. Bosmeny, Adam A. White, et al. "High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples." Journal of Biological Methods 8, no. 4 (2021): 1. http://dx.doi.org/10.14440/jbm.2021.360.

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In late 2019, a novel coronavirus began spreading in Wuhan, China, causing a potentially lethal respiratory viral infection. By early 2020, the novel coronavirus, called SARS-CoV-2, had spread globally, causing the COVID-19 pandemic. The infection and mutation rates of SARS-CoV-2 make it amenable to tracking introduction, spread and evolution by viral genome sequencing. Efforts to develop effective public health policies, therapeutics, or vaccines to treat or prevent COVID-19 are also expected to benefit from tracking mutations of the SARS-CoV-2 virus. Here we describe a set of comprehensive w
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25

Bhaduri, Aparna, Kun Qu, Carolyn S. Lee, Alexander Ungewickell, and Paul A. Khavari. "Rapid identification of non-human sequences in high-throughput sequencing datasets." Bioinformatics 28, no. 8 (2012): 1174–75. https://doi.org/10.5281/zenodo.13526446.

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(Uploaded by Plazi for the Bat Literature Project) UNLABELLED: Rapid identification of non-human sequences (RINS) is an intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of non-human sequences in deep sequencing datasets. In <2 h, RINS correctly identified the known virus in the dataset SRR73726 and is compatible with any computer capable of running the prerequisite alignment and assembly programs. RINS accurately identifies sequencing reads from intact or mutated non-human genomes in a dataset and robustly generates
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26

Bhaduri, Aparna, Kun Qu, Carolyn S. Lee, Alexander Ungewickell, and Paul A. Khavari. "Rapid identification of non-human sequences in high-throughput sequencing datasets." Bioinformatics 28, no. 8 (2012): 1174–75. https://doi.org/10.5281/zenodo.13526446.

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(Uploaded by Plazi for the Bat Literature Project) UNLABELLED: Rapid identification of non-human sequences (RINS) is an intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of non-human sequences in deep sequencing datasets. In <2 h, RINS correctly identified the known virus in the dataset SRR73726 and is compatible with any computer capable of running the prerequisite alignment and assembly programs. RINS accurately identifies sequencing reads from intact or mutated non-human genomes in a dataset and robustly generates
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27

Bhaduri, Aparna, Kun Qu, Carolyn S. Lee, Alexander Ungewickell, and Paul A. Khavari. "Rapid identification of non-human sequences in high-throughput sequencing datasets." Bioinformatics 28, no. 8 (2012): 1174–75. https://doi.org/10.5281/zenodo.13526446.

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(Uploaded by Plazi for the Bat Literature Project) UNLABELLED: Rapid identification of non-human sequences (RINS) is an intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of non-human sequences in deep sequencing datasets. In <2 h, RINS correctly identified the known virus in the dataset SRR73726 and is compatible with any computer capable of running the prerequisite alignment and assembly programs. RINS accurately identifies sequencing reads from intact or mutated non-human genomes in a dataset and robustly generates
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28

Bhaduri, Aparna, Kun Qu, Carolyn S. Lee, Alexander Ungewickell, and Paul A. Khavari. "Rapid identification of non-human sequences in high-throughput sequencing datasets." Bioinformatics 28, no. 8 (2012): 1174–75. https://doi.org/10.5281/zenodo.13526446.

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(Uploaded by Plazi for the Bat Literature Project) UNLABELLED: Rapid identification of non-human sequences (RINS) is an intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of non-human sequences in deep sequencing datasets. In <2 h, RINS correctly identified the known virus in the dataset SRR73726 and is compatible with any computer capable of running the prerequisite alignment and assembly programs. RINS accurately identifies sequencing reads from intact or mutated non-human genomes in a dataset and robustly generates
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29

Seo, Seung, Xiangpei Zeng, Mourad Assidi, et al. "High throughput whole mitochondrial genome sequencing by two platforms of massively parallel sequencing." BMC Genomics 15, Suppl 2 (2014): P7. http://dx.doi.org/10.1186/1471-2164-15-s2-p7.

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30

Sardaraz, Muhammad, Muhammad Tahir, and Ataul Aziz Ikram. "Advances in high throughput DNA sequence data compression." Journal of Bioinformatics and Computational Biology 14, no. 03 (2016): 1630002. http://dx.doi.org/10.1142/s0219720016300021.

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Advances in high throughput sequencing technologies and reduction in cost of sequencing have led to exponential growth in high throughput DNA sequence data. This growth has posed challenges such as storage, retrieval, and transmission of sequencing data. Data compression is used to cope with these challenges. Various methods have been developed to compress genomic and sequencing data. In this article, we present a comprehensive review of compression methods for genome and reads compression. Algorithms are categorized as referential or reference free. Experimental results and comparative analys
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31

Jarlier, Frédéric, Nicolas Joly, Nicolas Fedy, et al. "QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing." F1000Research 9 (April 6, 2020): 240. http://dx.doi.org/10.12688/f1000research.22954.1.

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Life science has entered the so-called ’big data era’ where biologists, clinicians and bioinformaticians are overwhelmed with unprecedented amount of data. High-throughput sequencing has revolutionized genomics and offers new insights to decipher the genome structure. However, using these data for daily clinical practice care and diagnosis purposes is challenging as the data are bigger and bigger. Therefore, we implemented software using Message Passing Interface such that the alignment and sorting of sequencing reads can easily scale on high-performance computing architecture. Our implementat
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32

Soylev, Arda, Thong Minh Le, Hajar Amini, Can Alkan, and Fereydoun Hormozdiari. "Discovery of tandem and interspersed segmental duplications using high-throughput sequencing." Bioinformatics 35, no. 20 (2019): 3923–30. http://dx.doi.org/10.1093/bioinformatics/btz237.

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Abstract Motivation Several algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, deletions and short inversions. In fact, complex SVs are of crucial importance and several have been associated with genomic disorders. To better understand the contribution of complex SVs to human disease, we need new algorithms to accurately discover and genotype such variants. Additionally, due to similar sequencing signatures, inverted dupli
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33

Jain, Akshita, Tongda Li, John Wainer, Jacqueline Edwards, Brendan C. Rodoni, and Timothy I. Sawbridge. "High-Throughput Sequencing Enables Rapid Analyses of Nematode Mitochondrial Genomes from an Environmental Sample." Pathogens 14, no. 3 (2025): 234. https://doi.org/10.3390/pathogens14030234.

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Mitochondrial genomes serve as essential tools in evolutionary biology, phylogenetics, and population genetics due to their maternal inheritance, lack of recombination, and conserved structure. Traditional morphological methods for identifying nematodes are often insufficient for distinguishing cryptic species complexes. This study highlights recent advancements in nematode mitochondrial genome research, particularly the impact of long-read sequencing technologies such as Oxford Nanopore. These technologies have facilitated the assembly of mitochondrial genomes from mixed soil samples, overcom
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34

Saeed, Muhammad, Zainab Jamil, Tayyab Shehzad, et al. "Role of Next Generation Sequencing (NGS) in Plant Disease Management: A Review." Journal of Applied Research in Plant Sciences 4, no. 01 (2023): 512–17. http://dx.doi.org/10.38211/joarps.2023.04.01.61.

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A high throughput technique used to determine a part of the nucleotide sequence of an organism’s genome is called next generation sequencing (NGS). NGS has been Proven revolutionary in genomics. Clinical diagnostics, Plant diseases diagnostic and other aspects of medical are now made possible by sequencing. Techniques of NGS: there are different techniques of NGS which are being used in real life sciences i.e., Illumina sequencing, Pyrosequencing, Roche 454 sequencing and Ion torrent sequencing. All vintage methods like culturing in bacterial, fungal, and viral samples are being suppressed by
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35

Georgiou, Georgios, and Simon J. van Heeringen. "fluff: exploratory analysis and visualization of high-throughput sequencing data." PeerJ 4 (July 19, 2016): e2209. http://dx.doi.org/10.7717/peerj.2209.

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Summary.In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can
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36

Jarlier, Frédéric, Nicolas Joly, Nicolas Fedy, et al. "QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing." F1000Research 9 (June 23, 2020): 240. http://dx.doi.org/10.12688/f1000research.22954.2.

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Life science has entered the so-called 'big data era' where biologists, clinicians and bioinformaticians are overwhelmed with high-throughput sequencing data. While they offer new insights to decipher the genome structure they also raise major challenges to use them for daily clinical practice care and diagnosis purposes as they are bigger and bigger. Therefore, we implemented a software to reduce the time to delivery for the alignment and the sorting of high-throughput sequencing data. Our solution is implemented using Message Passing Interface and is intended for high-performance computing a
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37

Jarlier, Frédéric, Nicolas Joly, Nicolas Fedy, et al. "QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing." F1000Research 9 (October 8, 2020): 240. http://dx.doi.org/10.12688/f1000research.22954.3.

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Life science has entered the so-called 'big data era' where biologists, clinicians and bioinformaticians are overwhelmed with high-throughput sequencing data. While they offer new insights to decipher the genome structure they also raise major challenges to use them for daily clinical practice care and diagnosis purposes as they are bigger and bigger. Therefore, we implemented a software to reduce the time to delivery for the alignment and the sorting of high-throughput sequencing data. Our solution is implemented using Message Passing Interface and is intended for high-performance computing a
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38

Zhu, Jiang, Mu Su, Yue Gu, et al. "Development of a method for identifying and functionally analyzing allele-specific DNA methylation based on BS-seq data." Epigenomics 11, no. 15 (2019): 1679–92. http://dx.doi.org/10.2217/epi-2019-0023.

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Aim: To comprehensively identify allele-specific DNA methylation (ASM) at the genome-wide level. Methods: Here, we propose a new method, called GeneASM, to identify ASM using high-throughput bisulfite sequencing data in the absence of haplotype information. Results: A total of 2194 allele-specific DNA methylated genes were identified in the GM12878 lymphocyte lineage using GeneASM. These genes are mainly enriched in cell cytoplasm function, subcellular component movement or cellular linkages. GM12878 methylated DNA immunoprecipitation sequencing, and methylation sensitive restriction enzyme se
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39

Zhou, Shaoyu, Keyaunoosh Kassauei, David J. Cutler, et al. "An Oligonucleotide Microarray for High-Throughput Sequencing of the Mitochondrial Genome." Journal of Molecular Diagnostics 8, no. 4 (2006): 476–82. http://dx.doi.org/10.2353/jmoldx.2006.060008.

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40

Teber, S., K. Gürcan, M. Akbulut, M. Abbasov, and S. Ercişli. "High-throughput whole genome sequencing of apricot (Prunus armeniaca) cultivar ‘Hacıhaliloğlu’." Acta Horticulturae, no. 1290 (September 2020): 53–58. http://dx.doi.org/10.17660/actahortic.2020.1290.10.

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41

Pan, Yonglong, Xiaoming Wang, Lin Liu, Hao Wang, and Meizhong Luo. "Whole Genome Mapping with Feature Sets from High-Throughput Sequencing Data." PLOS ONE 11, no. 9 (2016): e0161583. http://dx.doi.org/10.1371/journal.pone.0161583.

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42

Li, Ning, Mingzhi Ye, Yingrui Li, et al. "Whole genome DNA methylation analysis based on high throughput sequencing technology." Methods 52, no. 3 (2010): 203–12. http://dx.doi.org/10.1016/j.ymeth.2010.04.009.

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43

Incarnato, Danny, and Francesco Neri. "High-throughput whole-genome sequencing of E14 mouse embryonic stem cells." Genomics Data 3 (March 2015): 6–7. http://dx.doi.org/10.1016/j.gdata.2014.10.023.

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44

Sundquist, Andreas, Mostafa Ronaghi, Haixu Tang, Pavel Pevzner, and Serafim Batzoglou. "Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies." PLoS ONE 2, no. 5 (2007): e484. http://dx.doi.org/10.1371/journal.pone.0000484.

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45

Green, Richard E., Anna-Sapfo Malaspinas, Johannes Krause, et al. "A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing." Cell 134, no. 3 (2008): 416–26. http://dx.doi.org/10.1016/j.cell.2008.06.021.

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46

Hoffman, Joseph I., Fraser Simpson, Patrice David, et al. "High-throughput sequencing reveals inbreeding depression in a natural population." Proceedings of the National Academy of Sciences 111, no. 10 (2014): 3775–80. http://dx.doi.org/10.1073/pnas.1318945111.

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Proxy measures of genome-wide heterozygosity based on approximately 10 microsatellites have been used to uncover heterozygosity fitness correlations (HFCs) for a wealth of important fitness traits in natural populations. However, effect sizes are typically very small and the underlying mechanisms remain contentious, as a handful of markers usually provides little power to detect inbreeding. We therefore used restriction site associated DNA (RAD) sequencing to accurately estimate genome-wide heterozygosity, an approach transferrable to any organism. As a proof of concept, we first RAD sequenced
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47

GIZA, ALEKSANDRA, EWELINA IWAN, and DARIUSZ WASYL. "Application of high throughput sequencing in veterinary science." Medycyna Weterynaryjna 78, no. 02 (2022): 6622–2022. http://dx.doi.org/10.21521/mw.6622.

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High throughput sequencing (HTS) creates an opportunity for comprehensive genomic studies. It can be applied in veterinary science, bacteriology and virology, diagnostics of animal diseases, food safety, examinations of the composition of environmental samples, and even in veterinary vaccinology. Thus HTS a wide-ranging method that can be applied in different areas of the One Health approach. In particular, the whole genome sequencing (WGS) of bacteria is routinely used in food hygiene and outbreak investigations for phylogenetic analysis of pathogenic bacteria isolated from various sources ac
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48

Highlander, Sarah K. "High throughput sequencing methods for microbiome profiling: application to food animal systems." Animal Health Research Reviews 13, no. 1 (2012): 40–53. http://dx.doi.org/10.1017/s1466252312000126.

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AbstractAnalysis of microbial communities using high throughput sequencing methods began in the mid 2000s permitting the production of 1000s to 10,000s of sequence reads per sample and megabases of data per sequence run. This then unprecedented depth of sequencing allowed, for the first time, the discovery of the ‘rare biosphere’ in environmental samples. The technology was quickly applied to studies in several human subjects. Perhaps these early studies served as a reminder that though the microbes that inhabit mammals are known to outnumber host cells by an order of magnitude or more, most o
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49

Prasanna, HC, N. Rai, Zakir Hussain, Suresh R. Yerasu, and Jagesh K. Tiwari. "Tomato: Breeding and Genomics." Vegetable Science 50, Special (2023): 146–55. http://dx.doi.org/10.61180/vegsci.2023.v50.spl.02.

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Tomato is an important vegetable of the human diet. In tomatoes, through conventional breeding methods, many cultivars with desirable traits have been developed. With the advancement in sequencing technologies combined with reducing cost per sample, high-throughput genotyping platforms and bioinformatics pipelines have revolutionized tomato improvement. After the tomato genome sequencing in 2012, thousands of cultivated and wild species have been sequenced with respect to studies on population structure, genetic diversity, high-density maps and structural variants analysis so on. Now, genomics
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50

Massé, Delphine, Thierry Candresse, Denis Filloux, et al. "Characterization of Six Ampeloviruses Infecting Pineapple in Reunion Island Using a Combination of High-Throughput Sequencing Approaches." Viruses 16, no. 7 (2024): 1146. http://dx.doi.org/10.3390/v16071146.

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The cultivation of pineapple (Ananas comosus) is threatened worldwide by mealybug wilt disease of pineapple (MWP), whose etiology is not yet fully elucidated. In this study, we characterized pineapple mealybug wilt-associated ampeloviruses (PMWaVs, family Closteroviridae) from a diseased pineapple plant collected from Reunion Island, using a high-throughput sequencing approach combining Illumina short reads and Nanopore long reads. Reads co-assembly resulted in complete or near-complete genomes for six distinct ampeloviruses, including the first complete genome of pineapple mealybug wilt-assoc
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