Article
Biochemical Research Methods
Son Hoang Nguyen, Minh Duc Cao, Lachlan J. M. Coin
Summary: npGraph is a streaming hybrid assembly tool that uses assembly graph instead of separate pre-assembly contigs, resulting in more complete genome assembly by resolving the path finding problem on the assembly graph using long reads as the traversing guide. It provides a real-time visualization of the progress of assembly and maintains a low computational cost.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Marcela A. Johnson, Boris A. Vinatzer, Song Li
Summary: Climate change may result in the emergence of new plant diseases caused by unknown pathogens. Surveillance for emerging plant diseases is crucial to reduce threats to food security. Machine learning can be used for reference-free detection of plant pathogens using genomic sequencing.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mikang Sim, Jongin Lee, Daehong Kwon, Daehwan Lee, Nayoung Park, Suyeon Wy, Younhee Ko, Jaebum Kim
Summary: RBRC is a new read-clustering algorithm that improves de novo microbial genome assembly by accurately estimating read proximity. It has shown excellent performance in simulation-based evaluation and application to real genomes, improving assembly quality without additional sequencing data. RBRC can be used to generate high-quality microbial strain genome assemblies when genome assemblies of related strains are available, and to upgrade existing microbial genome assemblies when additional sequencing data, such as long reads, are difficult to obtain.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Gina V. Filloramo, Bruce A. Curtis, Emma Blanche, John M. Archibald
Summary: The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity, and ecology of the algal group. Long-read sequencing technology was used to update and validate the quality and contiguity of their genomes, leading to the resolution of uncertain genomic regions and identification of novel genes. Despite the challenges posed by repetitive DNA sequences, the revised reference genomes provide additional insight into the structure and evolution of these genomes for future diatom research.
Article
Biology
Hak-Min Kim, Sungwon Jeon, Oksung Chung, Je Hoon Jun, Hui-Su Kim, Asta Blazyte, Hwang-Yeol Lee, Youngseok Yu, Yun Sung Cho, Dan M. Bolser, Jong Bhak
Summary: The study compared 7 sequencing platforms using the same KOREF sample, and found that MGI platforms showed higher concordance rates for SNP genotyping compared to HiSeq2000 and HiSeq4000. The MGI platforms were also found to have the most similar characteristics to the HiSeq2500 platform according to a similarity matrix of variant calls. Overall, MGI and Illumina sequencing platforms showed comparable levels of sequencing quality, coverage uniformity, percent GC coverage, and variant accuracy, with MGI platforms being cost-effective for a wide range of genomics research fields.
Article
Biochemical Research Methods
Aidan P. Tay, Joshua J. Hamey, Gabriella E. Martyn, Laurence O. W. Wilson, Marc R. Wilkins
Summary: This study investigated the use of long-read, nanopore-based, direct RNA sequencing for the identification of protein isoforms in human K562 cells. The results showed that this approach outperformed short-read RNA sequencing in identifying alternative splicing events and protein isoforms. The study also highlighted the benefits of using long-read RNA sequencing data in generating reference databases for the identification of protein isoforms.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Oncology
Zoe Welham, Jun Li, Alexander F. Engel, Mark P. Molloy
Summary: This study compared two different DNA sequencing technologies to identify the gut microbiome in patients with or without bowel polyps. The results showed that different sequencing technologies and bioinformatics processing can affect the classification of gut microbiota. Although there were minor differences in gut microbiome between patients with and without bowel polyps, Ruminococcus gnavus, a bacteria associated with inflammatory bowel disease, was found to be more abundant in polyp patients.
Article
Immunology
Katherine J. L. Jackson, Justin T. Kos, William Lees, William S. Gibson, Melissa Laird Smith, Ayelet Peres, Gur Yaari, Martin Corcoran, Christian E. Busse, Mats Ohlin, Corey T. Watson, Andrew M. Collins
Summary: The poorly characterized immunoglobulin genes in inbred mouse strains commonly used in models of antibody-mediated human diseases could compromise data analysis. This study used long-read SMRT sequencing to amplify VDJ-C sequences from BALB/c mice and identified strain variations in specific immunoglobulin genes. By computationally retrieving IGHV haplotypes, a set of expressed BALB/c IGHV germline gene sequences was established. The study also assessed the suitability of assemblies from the Mouse Genome Project for the determination of IGH loci genes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Fan Jiang, Ai-Ping Mao, Yin-Yin Liu, Feng-Zhi Liu, Yan-Lin Li, Jian Li, Jian-Ying Zhou, Xue-Wei Tang, Ai-Ping Ju, Fa-Tao Li, Jun-Hui Wan, Lian-Dong Zuo, Dong-Zhi Li
Summary: In this study, we utilized single-molecule real-time (SMRT) sequencing to uncover rare thalassemia mutations in nine patients and their family members. The results demonstrate the importance of SMRT sequencing in thalassemia screening and diagnosis, particularly for detecting rare mutations.
Article
Multidisciplinary Sciences
Ka Ming Nip, Saber Hafezqorani, Kristina K. Gagalova, Readman Chiu, Chen Yang, Rene L. Warren, Inanc Birol
Summary: Long-read sequencing technologies have greatly improved, but there is little focus on reference-free transcriptome assembly methods. In this study, the authors introduce RNA-Bloom2, a reference-free method for long-read transcriptome sequencing data. They demonstrate its competitive assembly quality compared to reference-based methods, as well as its lower memory and runtime requirements. They also showcase its application in assembling a transcriptome sample of Sitka spruce, setting the groundwork for large-scale comparative transcriptomics without readily available genome assemblies.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Waleed Javaid, Jordan Ehni, Ana S. Gonzalez-Reiche, Juan Manuel Carreno, Elena Hirsch, Jessica Tan, Zenab Khan, Divya Kriti, Thanh Ly, Bethany Kranitzky, Barbara Barnett, Freddy Cera, Lenny Prespa, Marie Moss, Randy A. Albrecht, Ala Mustafa, Ilka Herbison, Matthew M. Hernandez, Theodore R. Pak, Hala A. Alshammary, Robert Sebra, Melissa L. Smith, Florian Krammer, Melissa R. Gitman, Emilia Mia Sordillo, Viviana Simon, Harm van Bakel
Summary: In early 2019, a large nosocomial influenza A virus outbreak was traced back to a single patient rather than healthcare workers, as initially assumed based on conventional epidemiology, using a combination of conventional surveillance with IAV genome sequencing and mining of electronic records.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Genetics & Heredity
Jared Johnson, Marty Soehnlen, Heather M. Blankenship
Summary: This study investigated the relationship between plasmid size and plasmid recovery by long-read-only assemblers Flye, Raven, Miniasm, and Canu. Oxford Nanopore long reads were used to determine the number of times each assembler successfully recovered 33 plasmids from 14 bacterial isolates of six bacterial genera, ranging in size from 1919 to 194,062 bp. Results showed Canu, Flye, Miniasm, and Raven were prone to missing plasmid sequences, while Unicycler successfully recovered 100% of plasmid sequences. It is recommended to use Unicycler to increase the likelihood of plasmid recovery during bacterial genome assembly.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Pauline Tremeaux, Justine Latour, Noemie Ranger, Venicia Ferrer, Agnes Harter, Romain Carcenac, Pauline Boyer, Sofia Demmou, Florence Nicot, Stephanie Raymond, Jacques Izopet
Summary: Co-infection with multiple strains of SARS-CoV-2, including Delta/Omicron and Omicron/Omicron co-infections, has been detected using long-read SMRT sequencing. These co-infections have implications for genetic diversification and virus evolution.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Yiqin Bai, Weili Lin, Jie Xu, Jun Song, Dongshan Yang, Y. Eugene Chen, Lin Li, Yixue Li, Zhen Wang, Jifeng Zhang
Summary: This study presented a new rabbit genome assembly UM_NZW_1.0 with improved continuity and gene annotations compared to the previous reference genome OryCun2.0, making it a valuable resource for future research on rabbits.
Article
Genetics & Heredity
Erdi Kucuk, Bart P. G. H. van der Sanden, Luke O'Gorman, Michael Kwint, Ronny Derks, Aaron M. Wenger, Christine Lambert, Shreyasee Chakraborty, Primo Baybayan, William J. Rowell, Han G. Brunner, Lisenka E. L. M. Vissers, Alexander Hoischen, Christian Gilissen
Summary: Long-read sequencing techniques have been successful in identifying structural variants. However, the high error rate of these techniques makes detecting small variants challenging. The introduction of PacBio HiFi sequencing allows for the detection of small variations. This study evaluates the ability of HiFi sequencing to detect de novo mutations of all types.