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genome sequence assembly algorithms and misassembly identification methods

MOLECULAR BIOLOGY REPORTS 2022年第11期49卷 11133-11148页

作者： Meng, Yue Lei, Yu Gao, Jianlong Liu, Yuxuan Ma, Enze Ding, Yunhong Bian, Yixin Zu, Hongquan Dong, Yucui Zhu, Xiao Yantai Univ Sch Comp & Control Engn Yantai Shandong Peoples R China Zhengzhou Univ Ind Technol Sch Informat Engn Zhengzhou Henan Peoples R China Harbin Normal Univ Sch Comp Sci & Informat Engn Harbin Heilongjiang Peoples R China Shanxi Inst Technol Dept Big Data & Intelligent Engn Yangquan Shanxi Peoples R China Harbin Inst Technol Ctr Network & Informat Harbin Heilongjiang Peoples R China Binzhou Med Univ Dept Immunol Yantai Shandong Peoples R China

The sequence assembly algorithms have rapidly evolved with the vigorous growth of genome sequencing technology over the past two decades. assembly mainly uses the iterative expansion of overlap relationships between sequences to construct the target genome. The assembly algorithms can be typically classified into several categories, such as the Greedy strategy, Overlap-Layout-Consensus (OLC) strategy, and de Bruijn graph (DBG) strategy. In particular, due to the rapid development of third-generation sequencing (TGS) technology, some prevalent assembly algorithms have been proposed to generate high-quality chromosome-level assemblies. However, due to the genome complexity, the length of short reads, and the high error rate of long reads, contigs produced by assembly may contain misassemblies adversely affecting downstream data analysis. Therefore, several read-based and reference-based methods for misassembly identification have been developed to improve assembly quality. This work primarily reviewed the development of DNA sequencing technologies and summarized sequencing data simulation methods, sequencing error correction methods, various mainstream sequence assembly algorithms, and misassembly identification methods. A large amount of computation makes the sequence assembly problem more challenging, and therefore, it is necessary to develop more efficient and accurate assembly algorithms and alternative algorithms.

关键词： genome assembly algorithms Misassembly identification methods genome sequencing technology Third-generation sequencing

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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

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NATURE BIOTECHNOLOGY 2024年第3期42卷 367-370页

作者： Lariviere, Delphine Abueg, Linelle Brajuka, Nadolina Gallardo-Alba, Cristobal Gruening, Bjorn Ko, Byung June Ostrovsky, Alex Palmada-Flores, Marc Pickett, Brandon D. Rabbani, Keon Antunes, Agostinho Balacco, Jennifer R. Chaisson, Mark J. P. Cheng, Haoyu Collins, Joanna Couture, Melanie Denisova, Alexandra Fedrigo, Olivier Gallo, Guido Roberto Giani, Alice Maria Gooder, Grenville MacDonald Horan, Kathleen Jain, Nivesh Johnson, Cassidy Kim, Heebal Lee, Chul Marques-Bonet, Tomas O'Toole, Brian Rhie, Arang Secomandi, Simona Sozzoni, Marcella Tilley, Tatiana Uliano-Silva, Marcela van den Beek, Marius Williams, Robert W. Waterhouse, Robert M. Phillippy, Adam M. Jarvis, Erich D. Schatz, Michael C. Nekrutenko, Anton Formenti, Giulio Penn State Univ Dept Biochem & Mol Biol University Pk PA 16802 USA Rockefeller Univ Vertebrate Genome Lab New York NY 10065 USA Albert Ludwigs Univ Freiburg Dept Comp Sci Bioinformat Grp Freiburg Germany Seoul Natl Univ Res Inst Agr & Life Sci Dept Agr Biotechnol Seoul South Korea Johns Hopkins Univ Dept Biol & Comp Sci Baltimore MD 21218 USA Univ Pompeu Fabra Inst Biol Evolut Dept Med & Life Sci MELIS CSIC Barcelona Spain NHGRI Computat & Stat Genom Branch Genome Informat Sect NIH Bethesda MD USA Univ Southern Calif Dept Quantitat & Computat Biol Los Angeles CA USA Univ Porto Interdisciplinary Ctr Marine & Environm Res CIIMAR CIMAR Porto Portugal Univ Porto Fac Sci Dept Biol Porto Portugal Dana Farber Canc Inst Dept Data Sci Boston MA USA Harvard Med Sch Dept Biomed Informat Boston MA USA Wellcome Sanger Inst Cambridge England Lomonosov Moscow State Univ Fac Bioengn & Bioinformat Moscow Russia Univ Milan Dept Biosci Milan Italy Weill Cornell Med Coll BMRI New York NY USA eGnome Inc Seoul South Korea Seoul Natl Univ Interdisciplinary Program Bioinformat Seoul South Korea Rockefeller Univ Lab Neurogenet Language New York NY USA Catalan Inst Res & Adv Studies ICREA Barcelona Spain Barcelona Inst Sci & Technol BIST Ctr Genom Regulat CRG CNAG Barcelona Spain Univ Autonoma Barcelona Inst Catala Paleontol Miquel Crusafont Cerdanyola Del Valles Spain Univ Cyprus Dept Biol Sci Nicosia Cyprus Univ Florence Dept Biol Florence Italy Wellcome Sanger Inst Tree Life Cambridge England Univ Tennessee Hlth Sci Ctr Dept Genet Genom & Informat Memphis TN USA Univ Lausanne Swiss Inst Bioinformat Dept Ecol & Evolut Lausanne Switzerland

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Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly

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NATURE METHODS 2024年第4期21卷 574-583页

作者： Darian, Joshua Casey Kundu, Ritu Rajaby, Ramesh Sung, Wing-Kin Natl Univ Singapore Sch Comp Singapore Singapore Genome Inst Singapore Singapore Singapore Chinese Univ Hong Kong Dept Chem Pathol Hong Kong Peoples R China Chinese Univ Hong Kong Li Ka Shing Inst Hlth Sci JC STEM Lab Computat Genom Hong Kong Peoples R China Hong Kong Genome Inst Hong Kong Peoples R China

Draft genomes generated from Oxford Nanopore Technologies (ONT) long reads are known to have a higher error rate. Although existing genome polishers can enhance their quality, the error rate (including mismatches, indels and switching errors between paternal and maternal haplotypes) can be significant. Here, we develop two polishers, hypo-short and hypo-hybrid to address this issue. Hypo-short utilizes Illumina short reads to polish an ONT-based draft assembly, resulting in a high-quality assembly with low error rates and switching errors. Expanding on this, hypo-hybrid incorporates ONT long reads to further refine the assembly into a diploid representation. Leveraging on hypo-hybrid, we have created a diploid genome assembly pipeline called hypo-assembler. Hypo-assembler automates the generation of highly accurate, contiguous and nearly complete diploid assemblies using ONT long reads, Illumina short reads and optionally Hi-C reads. Notably, our solution even allows for the production of telomere-to-telomere diploid genomes with additional manual steps. As a proof of concept, we successfully assembled a fully phased telomere-to-telomere diploid genome of HG00733, achieving a quality value exceeding 50. This work introduces two polishers for refining the draft genome generated from nanopore long reads, as well as an assembler pipeline for producing telomere-to-telomere diploid genome with low error rate.

关键词： genome assembly algorithms

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Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads

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NATURE BIOTECHNOLOGY 2022年第7期40卷 1075-+页

作者： Bankevich, Anton Bzikadze, Andrey V. Kolmogorov, Mikhail Antipov, Dmitry Pevzner, Pavel A. Univ Calif San Diego Dept Comp Sci & Engn San Diego CA 92103 USA Univ Calif San Diego Program Bioinformat & Syst Biol San Diego CA 92103 USA Univ Calif Santa Cruz Dept Biomol Engn Santa Cruz CA 95064 USA St Petersburg State Univ Inst Translat Biomed Ctr Algorithm Biotechnol St Petersburg Russia

A multiplex de Bruijn graph algorithm allows high-accuracy genome assembly from long, high-fidelity reads. Although most existing genome assemblers are based on de Bruijn graphs, the construction of these graphs for large genomes and large k-mer sizes has remained elusive. This algorithmic challenge has become particularly pressing with the emergence of long, high-fidelity (HiFi) reads that have been recently used to generate a semi-manual telomere-to-telomere assembly of the human genome. To enable automated assemblies of long, HiFi reads, we present the La Jolla Assembler (LJA), a fast algorithm using the Bloom filter, sparse de Bruijn graphs and disjointig generation. LJA reduces the error rate in HiFi reads by three orders of magnitude, constructs the de Bruijn graph for large genomes and large k-mer sizes and transforms it into a multiplex de Bruijn graph with varying k-mer sizes. Compared to state-of-the-art assemblers, our algorithm not only achieves five-fold fewer misassemblies but also generates more contiguous assemblies. We demonstrate the utility of LJA via the automated assembly of a human genome that completely assembled six chromosomes.

关键词： genome assembly algorithms

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Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

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NATURE GENETICS 2022年第3期54卷 342-+页

作者： Sun, Hequan Jiao, Wen-Biao Campoy, Jose A. Krause, Kristin Goel, Manish Folz-Donahue, Kat Kukat, Christian Huettel, Bruno Schneeberger, Korbinian Ludwig Maximilians Univ Munchen Fac Biol Planegg Martinsried Germany Max Planck Inst Plant Breeding Res Dept Chromosome Biol Cologne Germany Huazhong Agr Univ Minist Educ Key Lab Hort Plant Biol Wuhan Peoples R China Huazhong Agr Univ Coll Informat Wuhan Peoples R China Max Planck Inst Biol Ageing FACS & Imaging Core Facil Cologne Germany Max Planck Genome Ctr Cologne Cologne Germany Illumina Solut Ctr Berlin Berlin Germany

Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here,we report the 3.1Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar 'Otava' based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, similar to 50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving similar to 20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.

关键词： genome assembly algorithms genome informatics Genomics Plant breeding Biomedicine general Human Genetics Cancer Research Agriculture Gene Function Animal Genetics and Genomics

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Tuning parameters for polygenic risk score methods using GWAS summary statistics from training data

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NATURE COMMUNICATIONS 2024年第1期15卷 24页

作者： Jiang, Wei Chen, Ling Girgenti, Matthew J. Zhao, Hongyu Yale Sch Publ Hlth Dept Biostat New Haven CT 06510 USA Columbia Univ Dept Stat New York NY USA Yale Sch Med Dept Psychiat New Haven CT USA

Various polygenic risk scores (PRS) methods have been proposed to combine the estimated effects of single nucleotide polymorphisms (SNPs) to predict genetic risks for common diseases, using data collected from genome-wide association studies (GWAS). Some methods require external individual-level GWAS dataset for parameter tuning, posing privacy and security-related concerns. Leaving out partial data for parameter tuning can also reduce model prediction accuracy. In this article, we propose PRStuning, a method that tunes parameters for different PRS methods using GWAS summary statistics from the training data. PRStuning predicts the PRS performance with different parameters, and then selects the best-performing parameters. Because directly using training data effects tends to overestimate the performance in the testing data, we adopt an empirical Bayes approach to shrinking the predicted performance in accordance with the genetic architecture of the disease. Extensive simulations and real data applications demonstrate PRStuning's accuracy across PRS methods and parameters. Some polygenic risk score (PRS) methods for predicting genetic risk for common diseases require an external individual-level dataset for parameter tuning, posing privacy-related concerns. Here, the authors present an empirical Bayes method that tunes PRS models using only summary statistics from the training data.

关键词： Computational models genome assembly algorithms

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Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement

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NATURE GENETICS 2024年第5期56卷 992-1005页

作者： Wu, Xinyi Hu, Zhongyuan Zhang, Yan Li, Mao Liao, Nanqiao Dong, Junyang Wang, Baogen Wu, Jian Wu, Xiaohua Wang, Ying Wang, Jian Lu, Zhongfu Yang, Yi Sun, Yuyan Dong, Wenqi Zhang, Mingfang Li, Guojing Zhejiang Acad Agr Sci Inst Vegetables State Key Lab Managing Biot & Chem Threats Qual & Hangzhou Peoples R China Zhejiang Univ Coll Agr & Biotechnol Lab Vegetable Germplasm Innovat & Mol Breeding Hangzhou Peoples R China Guangdong Acad Agr Sci Vegetable Res Inst Guangdong Key Lab New Technol Res Vegetables Guangzhou Peoples R China Zhejiang Acad Agr Sci Minist Agr & Rural Affairs Key Lab Vegetable Legumes Germplasm Enhancement & Hangzhou Peoples R China Zhejiang Univ Yazhou Bay Sci & Technol City Hainan Inst Sanya Peoples R China Minist Agr & Rural Affairs Key Lab Hort Plant Growth & Dev Hangzhou Peoples R China

Cowpeas (tropical legumes) are important in ensuring food and nutritional security in developing countries, especially in sub-Saharan Africa. Herein, we report two high-quality genome assemblies of grain and vegetable cowpeas and we re-sequenced 344 accessions to characterize the genomic variations landscape. We identified 39 loci for ten important agronomic traits and more than 541 potential loci that underwent selection during cowpea domestication and improvement. In particular, the synchronous selections of the pod-shattering loci and their neighboring stress-relevant loci probably led to the enhancement of pod-shattering resistance and the compromise of stress resistance during the domestication from grain to vegetable cowpeas. Moreover, differential selections on multiple loci associated with pod length, grain number per pod, seed weight, pod and seed soluble sugars, and seed crude proteins shaped the yield and quality diversity in cowpeas. Our findings provide genomic insights into cowpea domestication and improvement footprints, enabling further genome-informed cultivar improvement of cowpeas. High-quality genome assemblies of grain and vegetable cowpeas and re-sequencing of 344 accessions characterize genomic variations between cowpea subspecies and their domestication and improvement under selection.

关键词： Genetic linkage study genome assembly algorithms genome-wide association studies Plant breeding

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Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea (MAY, 10.1038/s41588-024-01760-4, 2024)

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NATURE GENETICS 2024年第6期56卷 1320-1320页

作者： Khan, Aamir W. Garg, Vanika Sun, Shuai Gupta, Saurabh Dudchenko, Olga Roorkiwal, Manish Chitikineni, Annapurna Bayer, Philipp E. Shi, Chengcheng Upadhyaya, Hari D. Bohra, Abhishek Bharadwaj, Chellapilla Mir, Reyazul Rouf Baruch, Kobi Yang, Bicheng Coyne, Clarice J. Bansal, Kailash C. Nguyen, Henry T. Ronen, Gil Aiden, Erez Lieberman Veneklaas, Erik Siddique, Kadambot H. M. Liu, Xin Edwards, David Varshney, Rajeev K. Center of Excellence in Genomics and Systems Biology International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru India School of Biological Sciences University of Western Australia Perth Western Australia Australia Division of Plant Science and Technology University of Missouri Columbia MO USA Centre for Crop and Food Innovation WA State Agricultural Biotechnology Centre Food Futures Institute Murdoch University Murdoch Western Australia Australia BGI Research Qingdao China Curtin Health Innovation Research Institute (CHIRI) Curtin Medical School Curtin University Perth Western Australia Australia Department of Molecular and Human Genetics Center for Genome Architecture Baylor College of Medicine Houston TX USA Khalifa Center for Genetic Engineering and Biotechnology United Arab Emirates University Al-Ain United Arab Emirates Plant Genome Mapping Laboratory The University of Georgia Athens GA USA ICAR- Indian Agricultural Research Institute (IARI) New Delhi India Division of Genetics and Plant Breeding Faculty of Agriculture (FoA) SKUAST-KashmirWadura Campus Kashmir India NRGene Ltd Park HaMada Ness Ziona Israel BGI-Australia Herston Queensland Australia USDA-ARS Plant Germplasm Introduction and Testing Washington State University Pullman WA USA National Academy of Agricultural Sciences (NAAS) NASC Complex New Delhi India UWA Institute of Agriculture and School of Agriculture and Environment University of Western Australia Perth Western Australia Australia BGI Research Shenzhen China

Chickpea (Cicer arietinum L.)—an important legume crop cultivated in arid and semiarid regions—has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.

关键词： genome assembly algorithms Sequence annotation

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Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph

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NATURE METHODS 2024年第6期21卷 967-970页

作者： Cheng, Haoyu Asri, Mobin Lucas, Julian Koren, Sergey Li, Heng Dana Farber Canc Inst Dept Data Sci Boston MA 02215 USA Harvard Med Sch Dept Biomed Informat Boston MA 02115 USA Univ Calif Santa Cruz Genom Inst Santa Cruz CA USA Natl Human Genome Res Inst Genome Informat Sect Computat & Stat Genom Branch NIH Bethesda MD USA

Despite advances in long-read sequencing technologies, constructing a near telomere-to-telomere assembly is still computationally demanding. Here we present hifiasm (UL), an efficient de novo assembly algorithm combining multiple sequencing technologies to scale up population-wide near telomere-to-telomere assemblies. Applied to 22 human and two plant genomes, our algorithm produces better diploid assemblies at a cost of an order of magnitude lower than existing methods, and it also works with polyploid genomes. By effective and efficient integration of PacBio HiFi, Oxford Nanopore Technologies ultra-long and other sequencing data types, hifiasm (UL) enables telomere-to-telomere diploid and polyploid genome assembly at a population scale.

关键词： DNA sequencing genome assembly algorithms Genomics Software

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Creating diploid assemblies from Nanopore and Illumina reads with hypo-assembler

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NATURE METHODS 2024年第4期21卷 560-561页

作者： Darian, Joshua Casey Sung, Wing-Kin Natl Univ Singapore Singapore Singapore Chinese Univ Hong Kong Hong Kong Peoples R China

Diploid assembly is a difficult task that requires several types of genomic sequencing data, including - but not limited to - HiFi reads and parental sequences. Hypo-assembler, an assembly algorithm, uses high quality solid k-mers extracted from Illumina data alongside Nanopore reads to produce a high-quality diploid assembly using only Nanopore and Illumina data.

关键词： genome assembly algorithms Software

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