Article
Biochemical Research Methods
Ramin Shirali Hossein Zade, Aysun Urhan, Alvaro Assis de Souza, Akash Singh, Thomas Abeel
Summary: This study introduces a new tool called HAT for haplotype assembly, which utilizes short and long reads along with a reference genome to obtain higher-quality continuous haplotypes.
Article
Biochemical Research Methods
Heng Du, Chenguang Diao, Pengju Zhao, Lei Zhou, Jian-Feng Liu
Summary: By comparing 9 software programs and different types of sequencing reads, an optimized hybrid de novo assembly pipeline (HSCG) successfully constructed a draft genome for Duroc pig. Comparison with Sus scrofa 11.1 revealed important breakpoints in two genes. These findings contribute to pan-genome analysis studies and can serve as a guide for assembling other animal genomes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Francisca Rojas Ringeling, Shounak Chakraborty, Caroline Vissers, Derek Reiman, Akshay M. Patel, Ki-Heon Lee, Ari Hong, Chan-Woo Park, Tim Reska, Julien Gagneur, Hyeshik Chang, Maria L. Spletter, Ki-Jun Yoon, Guo-li Ming, Hongjun Song, Stefan Canzar
Summary: Ladder-seq is a method that improves the quality of RNA sequencing transcriptomes by separating transcripts by length before sequencing. Simulated data showed that Ladder-seq accurately quantifies transcripts of complex genes and has higher accuracy and sensitivity in transcript assembly. In experimental data, Ladder-seq identifies more genes with isoform switches and reveals widespread changes in isoform usage after m(6)A depletion.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Junwei Luo, Ting Guan, Guolin Chen, Zhonghua Yu, Haixia Zhai, Chaokun Yan, Huimin Luo
Summary: In this article, a hybrid scaffolding method (SLHSD) is introduced that combines the advantages of short reads and long reads to construct an optimal scaffold graph for assembly. Experimental results demonstrate that SLHSD outperforms other methods in terms of performance.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Cell Biology
Nataliya Timoshevskaya, Kaan Eskut, Vladimir A. Timoshevskiy, Sofia M. C. Robb, Carson Holt, Jon E. Hess, Hugo J. Parker, Cindy F. Baker, Allison K. Miller, Cody Saraceno, Mark Yandell, Robb Krumlauf, Shawn R. Narum, Ralph T. Lampman, Neil J. Gemmell, Jacquelyn Mountcastle, Bettina Haase, Jennifer R. Balacco, Giulio Formenti, Sarah Pelan, Ying Sims, Kerstin Howe, Olivier Fedrigo, Erich D. Jarvis, Jeramiah J. Smith
Summary: Programmed DNA loss is a gene silencing mechanism found in various vertebrate and nonvertebrate lineages. The evolution of somatically eliminated sequences in these species has been difficult to reconstruct due to repetitive and duplicated sequences. However, an improved assembly of the sea lamprey genome has enabled analysis that sheds light on the recruitment of genes to the germline-specific fraction and reveals the roles of segmental duplication and positive selection in the long-term evolution of germline-specific chromosomes.
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
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
Kez Cleal, Duncan M. Baird
Summary: Structural variation (SV) is important in genome evolution and disease, and Dysgu is a tool that accurately detects SVs using paired-end or long-read sequencing, with high sensitivity and fast running speed.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Xiongbin Kang, Xiao Luo, Alexander Schoenhuth
Summary: Next-generation sequencing allows for the identification of microorganisms in different habitats without the need for cultivation. However, distinguishing strains within a species is challenging due to minor genetic variations. This study introduces StrainXpress as a solution to reconstruct strain-specific genomes from metagenomes, and it successfully deals with poorly covered strains.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Andre Gohr, Luis P. Iniguez, Antonio Torres-Mendez, Sophie Bonnal, Manuel Irimia
Summary: Although splicing occurs co-transcriptionally, the order of intron removal is not necessarily sequential. Insplico is the first standalone software for quantifying the splicing order of adjacent introns (AISO) using both short and long read sequencing technologies. Insplico reveals biases associated with long read sequencing and identifies universal features of AISO patterns across different species. Additionally, Insplico uncovers non-canonical AISO in SRRM4-dependent microexons and suggests potential modes of SRRM4 regulation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Andrey D. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin, Julien Jarroux, Alla L. Lapidus, Hagen U. Tilgner
Summary: IsoQuant is a computational tool that uses intron graphs to accurately reconstruct transcripts with or without reference genome annotation. It reduces the false-positive rate by fivefold and 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively, for novel transcript discovery. IsoQuant also improves performance for Pacific Biosciences data.
NATURE BIOTECHNOLOGY
(2023)
Article
Biology
Arne Ludwig, Martin Pippel, Gene Myers, Michael Hiller
Summary: In this study, we present DENTIST, a sensitive, highly accurate, and automated pipeline method for closing gaps in short-read assemblies with long error-prone reads. Through tests on real genomic data, we demonstrate that DENTIST achieves higher accuracy and similar sensitivity compared to previous methods.
Article
Biotechnology & Applied Microbiology
Hyunji Lee, Jun Kim, Junho Lee
Summary: Recent advances in long-read sequencing technologies have enabled accurate identification of genetic variants. In this study, two Caenorhabditis elegans strains were used to compare the performance of two long-read sequencing platforms, HiFi and CLR. HiFi identified more true-positive variants and fewer false-positive variants compared to CLR. Additionally, assembly-based variant calling was shown to be effective for detection of large insertions using accurate long-read sequencing data.
Article
Genetics & Heredity
Jingjing Zhang, Md. Tofazzal Hossain, Weiguo Liu, Yin Peng, Yi Pan, Yanjie Wei
Summary: This study focuses on the functional study of circRNAs and evaluates the performance of several short-read sequence assembly algorithms using long-read sequences. A screening protocol is introduced to select circRNAs with full-length sequences. The results indicate that no single assembly algorithm performs better in all cases.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Guoshun Xu, Liwen Zhang, Xiaoqing Liu, Feifei Guan, Yuquan Xu, Haitao Yue, Jin-Qun Huang, Jieyin Chen, Ningfeng Wu, Jian Tian
Summary: This study compares the application of different DNA sequencing methods in soil metagenomics research. The results show that combining long-read and short-read data can increase the length of metagenomic sequences and gene pool, and has significant advantages in studying natural product biosynthetic genes in soil microbiomes.
Article
Genetics & Heredity
Michael Alonge, Alaina Shumate, Daniela Puiu, Aleksey Zimin, Steven L. Salzberg
Article
Biochemical Research Methods
Alaina Shumate, Steven L. Salzberg
Summary: Advancements in DNA sequencing and computational methods have led to a significant increase in high-quality genome assemblies for many species. To annotate gene features in these genomes, a common strategy is to map genes from a previously annotated reference genome to new or improved assemblies. The tool Liftoff can accurately map genes between the same or closely related species, ensuring high sequence identity and preserving gene structure.
Article
Multidisciplinary Sciences
Zhixing Feng, Jose C. Clemente, Brandon Wong, Eric E. Schadt
Summary: Cellular genetic heterogeneity is common across biological conditions, yet high error rates in long-read sequencing technologies limit their application to this subject. iGDA is introduced as a tool for accurate detection and phasing of minor variants, enabling precise haplotype reconstruction.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Aleksey Zimin, Alaina Shumate, Ida Shinder, Jakob Heinz, Daniela Puiu, Mihaela Pertea, Steven L. Salzberg
Summary: Until 2019, there was only one fully annotated version of the human genome. In 2019, a second individual genome was successfully assembled and annotated, which was from an individual of African descent. The new genome is more complete and contiguous than previous genomes.
Article
Multidisciplinary Sciences
Ariel Gershman, Michael E. G. Sauria, Xavi Guitart, Mitchell R. Vollger, Paul W. Hook, Savannah J. Hoyt, Miten Jain, Alaina Shumate, Roham Razaghi, Sergey Koren, Nicolas Altemose, Gina Caldas, Glennis A. Logsdon, Arang Rhie, Evan E. Eichler, Michael C. Schatz, Rachel J. O'Neill, Adam M. Phillippy, Karen H. Miga, Winston Timp
Summary: This study presents a high-resolution epigenetic analysis of the telomere-to-telomere human reference genome, revealing important insights into gene activity, clinical regulation, and providing a framework for investigating elusive regions of the genome.
Article
Multidisciplinary Sciences
Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J. Taylor, Kishwar Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, Nathan D. Olson, Michael E. G. Sauria, Mitchell R. Vollger, Arang Rhie, Melissa Meredith, Skylar Martin, Joyce Lee, Sergey Koren, Jeffrey A. Rosenfeld, Benedict Paten, Ryan Layer, Chen-Shan Chin, Fritz J. Sedlazeck, Nancy F. Hansen, Danny E. Miller, Adam M. Phillippy, Karen H. Miga, Rajiv C. McCoy, Megan Y. Dennis, Justin M. Zook, Michael C. Schatz
Summary: Compared to its predecessors, the Telomere-to-Telomere CHM13 genome has significant improvements in sequence length and structural accuracy, enabling more comprehensive study of the human genome. The application of the T2T-CHM13 reference has demonstrated improved accuracy in read mapping and variant calling for globally diverse samples, leading to the discovery of previously unresolved variants and the removal of false positives. These advancements position T2T-CHM13 as a potential replacement for GRCh38 as the dominant reference for human genetics.
Article
Biotechnology & Applied Microbiology
Xiao Liu, Weichen Song, Brandon Y. Wong, Ting Zhang, Shunying Yu, Guan Ning Lin, Xianting Ding