Article
Multidisciplinary Sciences
Ying Chen, Fan Nie, Shang-Qian Xie, Ying-Feng Zheng, Qi Dai, Thomas Bray, Yao-Xin Wang, Jian-Feng Xing, Zhi-Jian Huang, De-Peng Wang, Li-Juan He, Feng Luo, Jian-Xin Wang, Yi-Zhi Liu, Chuan-Le Xiao
Summary: The error correction and de novo assembly tool NECAT developed by the authors efficiently produces high-quality assemblies of nanopore reads. The tool utilizes adaptive read selection and a two-step progressive method to overcome the high error rates in nanopore reads.
NATURE COMMUNICATIONS
(2021)
Article
Evolutionary Biology
Daniel Frei, Elisabeth Veekman, Daniel Grogg, Ingrid Stoffel-Studer, Aki Morishima, Rie Shimizu-Inatsugi, Steven Yates, Kentaro K. Shimizu, Juerg E. Frey, Bruno Studer, Dario Copetti
Summary: Despite the challenges in reconstructing telomere-to-telomere genome assemblies of large and repeat-rich eukaryotic genomes, the optimization of Oxford Nanopore Technologies' sequencing protocol has successfully produced a high-quality and contiguous genome assembly of perennial ryegrass. The key factor in determining assembly contiguity was found to be read length. This protocol has the potential to enhance genomics-assisted breeding programs for forage grasses.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Immunology
Jinming Wang, Kai Chen, Qiaoyun Ren, Ying Zhang, Junlong Liu, Guangying Wang, Aihong Liu, Youquan Li, Guangyuan Liu, Jianxun Luo, Wei Miao, Jie Xiong, Hong Yin, Guiquan Guan
Summary: The study evaluated the performance of nine de novo assemblers for ONT on different coverage depth datasets. The results showed that coverage depth significantly affected genome quality, the level of contiguity varied among different tools, and genome correctness was related to completeness.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Dhaivat Joshi, Shunfu Mao, Sreeram Kannan, Suhas Diggavi
Summary: QAlign is designed as a pre-processor for aligning long reads to a genome/transcriptome or other long reads. By converting nucleotide reads into discretized current levels, QAlign significantly improves alignment rates and overlap quality.
Article
Virology
Yi Yan, Ke Wu, Jun Chen, Haizhou Liu, Yi Huang, Yong Zhang, Jin Xiong, Weipeng Quan, Xin Wu, Yu Liang, Kunlun He, Zhilong Jia, Depeng Wang, Di Liu, Hongping Wei, Jianjun Chen
Summary: Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic, with the ability to identify pathogens and trace virus genetics. Modifications to the approach using specific amplicon amplification and the Oxford Nanopore PromethION platform have enabled rapid and stable acquisition of high-quality SARS-CoV-2 genomes, as well as the detection of genetic mutations.
Article
Genetics & Heredity
Zuyu Yang, Andrea Guarracino, Patrick J. Biggs, Michael A. Black, Nuzla Ismail, Jana Renee Wold, Tony R. Merriman, Pjotr Prins, Erik Garrison, Joep de Ligt
Summary: Whole genome sequencing has revolutionized infectious disease surveillance. However, using a linear reference genome may introduce biases when studying highly variable bacterial genomes. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants, improving mapping rates and variant calling for pathogens such as Neisseria meningitidis.
FRONTIERS IN GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Jong Ghut Ashley Aw, Shaun W. Lim, Jia Xu Wang, Finnlay R. P. Lambert, Wen Ting Tan, Yang Shen, Yu Zhang, Pornchai Kaewsapsak, Chenhao Li, Sarah B. Ng, Leah A. Vardy, Meng How Tan, Niranjan Nagarajan, Yue Wan
Summary: PORE-cupine is a RNA structure analysis method that combines long-read RNA sequencing, structure probing, and machine learning to detect secondary structures in cellular RNAs and capture global structural features. The method reveals structural differences between distinct transcript isoforms of the same gene, highlighting the importance of understanding the role of structures in gene regulation.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, Gunjan Baid, Mikhail Kolmogorov, Jordan M. Eizenga, Karen H. Miga, Paolo Carnevali, Miten Jain, Andrew Carroll, Benedict Paten
Summary: The PEPPER-Margin-DeepVariant pipeline utilizes nanopore and other long-read sequencing data to achieve highly accurate variant calling, surpassing the limitations of short-read methods in chromosomal analysis.
Article
Biochemical Research Methods
Xiaowen Feng, Haoyu Cheng, Daniel Portik, Heng Li
Summary: hifiasm-meta is a software tool designed for assembling metagenomes using high-accuracy long-read data, which can reconstruct bacterial genomes in microbial communities more accurately.
Article
Biochemistry & Molecular Biology
Bingyan Li, Zhenyong Du, Li Tian, Limeng Zhang, Zhihua Huang, Shujun Wei, Fan Song, Wanzhi Cai, Yanbi Yu, Hailin Yang, Hu Li
Summary: The study constructed a high-quality reference genome of Aphidius gifuensis, revealing significantly expanded gene families involved in metabolic processes, cell signal communication, and other functions, along with contracted olfactory receptors. This provides a solid foundation for future research on the molecular mechanisms of population decline and host-parasitoid relationship for parasitoid wasps.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Genetics & Heredity
Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye
Summary: This study successfully assembled a high-quality and almost complete genome of Arabidopsis thaliana using multiple advanced sequencing technologies. The new genome assembly contains more information compared to the previous reference genome, providing valuable insights into the global pattern of centromeric polymorphisms and the genetic and epigenetic features in plants.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Annett Erkes, Rene P. Grove, Milena Zarkovic, Sebastian Krautwurst, Ralf Koebnik, Richard D. Morgan, Geoffrey G. Wilson, Martin Hoelzer, Manja Marz, Jens Boch, Jan Grau
Summary: This study successfully assembled the 5 Mbp genomes of five Xanthomonas strains using Oxford Nanopore Technologies (ONT) sequencing data, and developed a computational correction pipeline to correct errors in TALE genes. The results demonstrate that the combination of ONT sequencing and computational correction is a powerful tool for characterizing the TALomes of large collections of Xanthomonas strains.
Article
Genetics & Heredity
Ryan R. Wick, Louise M. Judd, Kelly L. Wyres, Kathryn E. Holt
Summary: This study compared the ligation and rapid approaches for bacterial whole-genome sequencing by Oxford Nanopore Technologies, finding that the rapid library preparation method is preferable for recovering small plasmid sequences. Sequencing DNA from seven plasmid-rich bacterial isolates using Illumina as a reference, it was observed that small plasmids were underrepresented in ligation read sets but not in rapid read sets. The results also showed lower rates of chimaeric reads in the rapid read sets compared to ligation read sets.
MICROBIAL GENOMICS
(2021)
Article
Biochemical Research Methods
Eleni Adam, Desh Ranjan, Harold Riethman
Summary: This article introduces a new method for genome assembly that combines Linked-Read data with nanopore reads to improve the accuracy and coverage of subtelomeric regions that are difficult to assemble. By combining Linked-Read sequences with nanopore reads, subtelomeric segmental duplications can be better assembled and assembly errors can be corrected. Experimental results demonstrate that this method can produce higher-quality and more complete assemblies compared to methods using only nanopore reads.
BMC BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Marine Salson, Julie Orjuela, Cedric Mariac, Leila Zekraoui, Marie Couderc, Sandrine Arribat, Nathalie Rodde, Adama Faye, Ndjido A. Kane, Christine Tranchant-Dubreuil, Yves Vigouroux, Cecile Berthouly-Salazar
Summary: An improved quality assembly of the pearl millet genome was obtained using long-read sequencing and optical maps, resulting in a more complete and higher quality assembly. This will greatly benefit research on structural variants, genomics studies, and pearl millet breeding.
G3-GENES GENOMES GENETICS
(2023)
Article
Multidisciplinary Sciences
Zichen Wang, Caroline D. Monteiro, Kathleen M. Jagodnik, Nicolas F. Fernandez, Gregory W. Gundersen, Andrew D. Rouillard, Sherry L. Jenkins, Axel S. Feldmann, Kevin S. Hu, Michael G. McDermott, Qiaonan Duan, Neil R. Clark, Matthew R. Jones, Yan Kou, Troy Goff, Holly Woodland, Fabio M. R. Amaral, Gregory L. Szeto, Oliver Fuchs, Sophia M. Schussler-Fiorenza Rose, Shvetank Sharma, Uwe Schwartz, Xabier Bengoetxea Bausela, Maciej Szymkiewicz, Vasileios Maroulis, Anton Salykin, Carolina M. Barra, Candice D. Kruth, Nicholas J. Bongio, Vaibhav Mathur, Radmila D. Todoric, Udi E. Rubin, Apostolos Malatras, Carl T. Fulp, John A. Galindo, Ruta Motiejunaite, Christoph Jueschke, Philip C. Dishuck, Katharina Lahl, Mohieddin Jafari, Sara Aibar, Apostolos Zaravinos, Linda H. Steenhuizen, Lindsey R. Allison, Pablo Gamallo, Fernando de Andres Segura, Tyler Dae Devlin, Vicente Perez-Garcia, Avi Ma'ayan
NATURE COMMUNICATIONS
(2016)
Article
Multidisciplinary Sciences
Glennis A. Logsdon, Mitchell R. Vollger, PingHsun Hsieh, Yafei Mao, Mikhail A. Liskovykh, Sergey Koren, Sergey Nurk, Ludovica Mercuri, Philip C. Dishuck, Arang Rhie, Leonardo G. de Lima, Tatiana Dvorkina, David Porubsky, William T. Harvey, Alla Mikheenko, Andrey Bzikadze, Milinn Kremitzki, Tina A. Graves-Lindsay, Chirag Jain, Kendra Hoekzema, Shwetha C. Murali, Katherine M. Munson, Carl Baker, Melanie Sorensen, Alexandra M. Lewis, Urvashi Surti, Jennifer L. Gerton, Vladimir Larionov, Mario Ventura, Karen H. Miga, Adam M. Phillippy, Evan E. Eichler
Summary: The study completed the linear assembly of human chromosome 8 using long-read sequencing technologies, resolving five long-standing gaps, including regions important for disease risk. The research revealed that the centromeric alpha-satellite sequence is generally methylated, and conducted comparative analysis of centromeres in chimpanzee, orangutan and macaque. The study estimates that the mutation rate of centromeric satellite DNA is accelerated compared to unique portions of the genome.
Article
Multidisciplinary Sciences
Pille Hallast, Peter Ebert, Mark Loftus, Feyza Yilmaz, Peter A. Audano, Glennis A. Logsdon, Marc Jan Bonder, Weichen Zhou, Wolfram Hoeps, Kwondo Kim, Chong Li, Savannah J. Hoyt, Philip C. Dishuck, David Porubsky, Fotios Tsetsos, Jee Young Kwon, Qihui Zhu, Katherine M. Munson, Patrick Hasenfeld, William T. Harvey, Alexandra P. Lewis, Jennifer Kordosky, Kendra Hoekzema, Rachel J. O'Neill, Jan O. Korbel, Chris Tyler-Smith, Evan E. Eichler, Xinghua Shi, Christine R. Beck, Tobias Marschall, Miriam K. Konkel, Charles Lee
Summary: De novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution reveal considerable diversity in the size and structure of the human Y chromosome. The male-specific euchromatic region is subject to large inversions with a higher recurrence rate compared to other chromosomes. Additionally, the study found extensive variation in the repeat arrays of the Y chromosome.
