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For: Yeo S, Coombe L, Warren RL, Chu J, Birol I. ARCS: scaffolding genome drafts with linked reads. Bioinformatics 2018;34:725-731. [PMID: 29069293 PMCID: PMC6030987 DOI: 10.1093/bioinformatics/btx675] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 10/20/2017] [Indexed: 01/12/2023]  Open
Number Cited by Other Article(s)
51
Maestri S, Gambino G, Lopatriello G, Minio A, Perrone I, Cosentino E, Giovannone B, Marcolungo L, Alfano M, Rombauts S, Cantu D, Rossato M, Delledonne M, Calderón L. 'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.). BMC Genomics 2022;23:159. [PMID: 35209840 PMCID: PMC8867635 DOI: 10.1186/s12864-022-08389-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/15/2022] [Indexed: 12/18/2022]  Open
52
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nat Commun 2022;13:682. [PMID: 35115520 PMCID: PMC8813957 DOI: 10.1038/s41467-022-28362-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022]  Open
53
Yang Y, Yoo JY, Baek SH, Song HY, Jo S, Jung SH, Choi JH. Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus. Gigascience 2022;11:giab089. [PMID: 35022698 PMCID: PMC8756193 DOI: 10.1093/gigascience/giab089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/08/2021] [Accepted: 12/05/2021] [Indexed: 11/28/2022]  Open
54
Visendi P. De Novo Assembly of Linked Reads Using Supernova 2.0. Methods Mol Biol 2022;2443:233-243. [PMID: 35037209 DOI: 10.1007/978-1-0716-2067-0_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
55
Stahlke AR, Bitume EV, Özsoy ZA, Bean DW, Veillet A, Clark MI, Clark EI, Moran P, Hufbauer RA, Hohenlohe PA. Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control. Evol Appl 2022;15:60-77. [PMID: 35126648 PMCID: PMC8792477 DOI: 10.1111/eva.13325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/31/2023]  Open
56
Liu Z, Roesti M, Marques D, Hiltbrunner M, Saladin V, Peichel CL. Chromosomal fusions facilitate adaptation to divergent environments in threespine stickleback. Mol Biol Evol 2021;39:6462204. [PMID: 34908155 PMCID: PMC8826639 DOI: 10.1093/molbev/msab358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
57
Guan D, McCarthy SA, Ning Z, Wang G, Wang Y, Durbin R. Efficient iterative Hi-C scaffolder based on N-best neighbors. BMC Bioinformatics 2021;22:569. [PMID: 34837944 PMCID: PMC8627104 DOI: 10.1186/s12859-021-04453-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 09/07/2021] [Indexed: 01/27/2023]  Open
58
Rahman A, Pachter L. SWALO: scaffolding with assembly likelihood optimization. Nucleic Acids Res 2021;49:e117. [PMID: 34417615 PMCID: PMC8599790 DOI: 10.1093/nar/gkab717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/16/2021] [Accepted: 08/16/2021] [Indexed: 01/01/2023]  Open
59
Lu CW, Yao CT, Hung CM. Domestication obscures genomic estimates of population history. Mol Ecol 2021;31:752-766. [PMID: 34779057 DOI: 10.1111/mec.16277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022]
60
Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL, Birol I. LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinformatics 2021;22:534. [PMID: 34717540 PMCID: PMC8557608 DOI: 10.1186/s12859-021-04451-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022]  Open
61
Chakraborty A, Mahajan S, Jaiswal SK, Sharma VK. Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. Commun Biol 2021;4:1193. [PMID: 34654884 PMCID: PMC8521574 DOI: 10.1038/s42003-021-02720-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 08/13/2021] [Indexed: 12/28/2022]  Open
62
Li K, Jiang W, Hui Y, Kong M, Feng LY, Gao LZ, Li P, Lu S. Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution. MOLECULAR PLANT 2021;14:1745-1756. [PMID: 34171481 DOI: 10.1016/j.molp.2021.06.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 05/04/2023]
63
Morisse P, Lemaitre C, Legeai F. LRez: a C++ API and toolkit for analyzing and managing Linked-Reads data. BIOINFORMATICS ADVANCES 2021;1:vbab022. [PMID: 36700107 PMCID: PMC9710615 DOI: 10.1093/bioadv/vbab022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/09/2021] [Accepted: 09/20/2021] [Indexed: 01/28/2023]
64
Freire R, Weisweiler M, Guerreiro R, Baig N, Hüttel B, Obeng-Hinneh E, Renner J, Hartje S, Muders K, Truberg B, Rosen A, Prigge V, Bruckmüller J, Lübeck J, Stich B. Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety. G3-GENES GENOMES GENETICS 2021;11:6371871. [PMID: 34534288 PMCID: PMC8664475 DOI: 10.1093/g3journal/jkab330] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/08/2021] [Indexed: 01/27/2023]
65
Sène MA, Kiesslich S, Djambazian H, Ragoussis J, Xia Y, Kamen AA. Haplotype-resolved de novo assembly of the Vero cell line genome. NPJ Vaccines 2021;6:106. [PMID: 34417462 PMCID: PMC8379168 DOI: 10.1038/s41541-021-00358-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 07/12/2021] [Indexed: 01/13/2023]  Open
66
Hiltunen M, Ryberg M, Johannesson H. ARBitR: an overlap-aware genome assembly scaffolder for linked reads. Bioinformatics 2021;37:2203-2205. [PMID: 33216122 PMCID: PMC8352505 DOI: 10.1093/bioinformatics/btaa975] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/22/2020] [Accepted: 11/10/2020] [Indexed: 12/02/2022]  Open
67
Yang X, Slotte T, Dainat J, Hambäck PA. Genome assemblies of three closely related leaf beetle species (Galerucella spp.). G3 (BETHESDA, MD.) 2021;11:6307723. [PMID: 34849825 PMCID: PMC8496278 DOI: 10.1093/g3journal/jkab214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
68
Genome of the world's smallest flowering plant, Wolffia australiana, helps explain its specialized physiology and unique morphology. Commun Biol 2021;4:900. [PMID: 34294872 PMCID: PMC8298427 DOI: 10.1038/s42003-021-02422-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/17/2021] [Indexed: 11/17/2022]  Open
69
Kim SH, Lee SJ, Jo E, Kim J, Kim JU, Kim JH, Park H, Chi YM. Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian. Animals (Basel) 2021;11:ani11072046. [PMID: 34359174 PMCID: PMC8300169 DOI: 10.3390/ani11072046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]  Open
70
Duckett DJ, Sullivan J, Pirro S, Carstens BC. Genomic Resources for the North American Water Vole (Microtus richardsoni) and the Montane Vole (Microtus montanus). GIGABYTE 2021;2021:gigabyte19. [PMID: 36824326 PMCID: PMC9631978 DOI: 10.46471/gigabyte.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/04/2021] [Indexed: 11/09/2022]  Open
71
Lopes M, Louzada S, Gama-Carvalho M, Chaves R. Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time. Int J Mol Sci 2021;22:4707. [PMID: 33946766 PMCID: PMC8125562 DOI: 10.3390/ijms22094707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022]  Open
72
Gavrielatos M, Kyriakidis K, Spandidos DA, Michalopoulos I. Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly. Mol Med Rep 2021;23:251. [PMID: 33537807 PMCID: PMC7893683 DOI: 10.3892/mmr.2021.11890] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/21/2021] [Indexed: 12/30/2022]  Open
73
Guo L, Xu M, Wang W, Gu S, Zhao X, Chen F, Wang O, Xu X, Seim I, Fan G, Deng L, Liu X. SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme. BMC Bioinformatics 2021;22:158. [PMID: 33765921 PMCID: PMC7993450 DOI: 10.1186/s12859-021-04081-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/16/2021] [Indexed: 12/30/2022]  Open
74
Mathers TC, Wouters RHM, Mugford ST, Swarbreck D, van Oosterhout C, Hogenhout SA. Chromosome-Scale Genome Assemblies of Aphids Reveal Extensively Rearranged Autosomes and Long-Term Conservation of the X Chromosome. Mol Biol Evol 2021;38:856-875. [PMID: 32966576 PMCID: PMC7947777 DOI: 10.1093/molbev/msaa246] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
75
Smith CH. A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). Genome Biol Evol 2021;13:evab029. [PMID: 33570560 PMCID: PMC7937423 DOI: 10.1093/gbe/evab029] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/16/2022]  Open
76
Luo J, Wei Y, Lyu M, Wu Z, Liu X, Luo H, Yan C. A comprehensive review of scaffolding methods in genome assembly. Brief Bioinform 2021;22:6149347. [PMID: 33634311 DOI: 10.1093/bib/bbab033] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/20/2022]  Open
77
Wang C, Wallerman O, Arendt ML, Sundström E, Karlsson Å, Nordin J, Mäkeläinen S, Pielberg GR, Hanson J, Ohlsson Å, Saellström S, Rönnberg H, Ljungvall I, Häggström J, Bergström TF, Hedhammar Å, Meadows JRS, Lindblad-Toh K. A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Commun Biol 2021;4:185. [PMID: 33568770 PMCID: PMC7875987 DOI: 10.1038/s42003-021-01698-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022]  Open
78
Biological computation and computational biology: survey, challenges, and discussion. Artif Intell Rev 2021. [DOI: 10.1007/s10462-020-09951-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
79
Gene Sequence Assembly Algorithm Model Based on the DBG Strategy and Its Application. JOURNAL OF HEALTHCARE ENGINEERING 2021. [DOI: 10.1155/2021/6676194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
80
Hruska JP, Manthey JD. De novo assembly of a chromosome-scale reference genome for the northern flicker Colaptes auratus. G3 (BETHESDA, MD.) 2021;11:jkaa026. [PMID: 33561233 PMCID: PMC8022726 DOI: 10.1093/g3journal/jkaa026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/12/2020] [Indexed: 11/15/2022]
81
Peona V, Blom MPK, Xu L, Burri R, Sullivan S, Bunikis I, Liachko I, Haryoko T, Jønsson KA, Zhou Q, Irestedt M, Suh A. Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise. Mol Ecol Resour 2021;21:263-286. [PMID: 32937018 PMCID: PMC7757076 DOI: 10.1111/1755-0998.13252] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 01/09/2023]
82
Doyle SR, Tracey A, Laing R, Holroyd N, Bartley D, Bazant W, Beasley H, Beech R, Britton C, Brooks K, Chaudhry U, Maitland K, Martinelli A, Noonan JD, Paulini M, Quail MA, Redman E, Rodgers FH, Sallé G, Shabbir MZ, Sankaranarayanan G, Wit J, Howe KL, Sargison N, Devaney E, Berriman M, Gilleard JS, Cotton JA. Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm. Commun Biol 2020;3:656. [PMID: 33168940 PMCID: PMC7652881 DOI: 10.1038/s42003-020-01377-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/14/2020] [Indexed: 12/31/2022]  Open
83
The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome. PLoS One 2020;15:e0240935. [PMID: 33119641 PMCID: PMC7595290 DOI: 10.1371/journal.pone.0240935] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]  Open
84
Biello R, Singh A, Godfrey CJ, Fernández FF, Mugford ST, Powell G, Hogenhout SA, Mathers TC. A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum Hausmann (Hemiptera: Aphididae). Mol Ecol Resour 2020;21:316-326. [PMID: 32985768 DOI: 10.1111/1755-0998.13258] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/21/2020] [Accepted: 09/07/2020] [Indexed: 01/18/2023]
85
Zhou Q, Tang D, Huang W, Yang Z, Zhang Y, Hamilton JP, Visser RGF, Bachem CWB, Robin Buell C, Zhang Z, Zhang C, Huang S. Haplotype-resolved genome analyses of a heterozygous diploid potato. Nat Genet 2020;52:1018-1023. [PMID: 32989320 PMCID: PMC7527274 DOI: 10.1038/s41588-020-0699-x] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
86
Hu J, Fan J, Sun Z, Liu S. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 2020;36:2253-2255. [PMID: 31778144 DOI: 10.1093/bioinformatics/btz891] [Citation(s) in RCA: 696] [Impact Index Per Article: 139.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 10/07/2019] [Accepted: 11/26/2019] [Indexed: 01/20/2023]  Open
87
Fuller ZL, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L, Peng J, Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M. Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science 2020;369:369/6501/eaba4674. [PMID: 32675347 DOI: 10.1126/science.aba4674] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
88
Colella JP, Tigano A, MacManes MD. A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues. Mol Ecol Resour 2020;20:856-870. [PMID: 32153100 PMCID: PMC7496956 DOI: 10.1111/1755-0998.13155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022]
89
Tolstoganov I, Bankevich A, Chen Z, Pevzner PA. cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs. Bioinformatics 2020;35:i61-i70. [PMID: 31510642 PMCID: PMC6612831 DOI: 10.1093/bioinformatics/btz349] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
90
Peng J, Li Q, Xu L, Wei P, He P, Zhang X, Zhang L, Guan J, Zhang X, Lin Y, Gui J, Chen X. Chromosome-level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune-related genes in bivalves. Mol Ecol Resour 2020;20:980-994. [PMID: 32198971 DOI: 10.1111/1755-0998.13157] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 03/09/2020] [Accepted: 03/16/2020] [Indexed: 12/30/2022]
91
Field MA, Rosen BD, Dudchenko O, Chan EKF, Minoche AE, Edwards RJ, Barton K, Lyons RJ, Tuipulotu DE, Hayes VM, D. Omer A, Colaric Z, Keilwagen J, Skvortsova K, Bogdanovic O, Smith MA, Aiden EL, Smith TPL, Zammit RA, Ballard JWO. Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. Gigascience 2020;9:giaa027. [PMID: 32236524 PMCID: PMC7111595 DOI: 10.1093/gigascience/giaa027] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/29/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]  Open
92
Karaoğlanoğlu F, Ricketts C, Ebren E, Rasekh ME, Hajirasouliha I, Alkan C. VALOR2: characterization of large-scale structural variants using linked-reads. Genome Biol 2020;21:72. [PMID: 32192518 PMCID: PMC7083023 DOI: 10.1186/s13059-020-01975-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/24/2020] [Indexed: 12/31/2022]  Open
93
Kyriakidou M, Anglin NL, Ellis D, Tai HH, Strömvik MV. Genome assembly of six polyploid potato genomes. Sci Data 2020;7:88. [PMID: 32161269 PMCID: PMC7066127 DOI: 10.1038/s41597-020-0428-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/14/2020] [Indexed: 02/06/2023]  Open
94
Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity. G3-GENES GENOMES GENETICS 2020;10:907-915. [PMID: 31988161 PMCID: PMC7056978 DOI: 10.1534/g3.119.400725] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
95
Í Kongsstovu S, Mikalsen SO, Homrum EÍ, Jacobsen JA, Flicek P, Dahl HA. Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly. Sci Rep 2019;9:17716. [PMID: 31776409 PMCID: PMC6881392 DOI: 10.1038/s41598-019-54151-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/08/2019] [Indexed: 01/01/2023]  Open
96
Luo J, Lyu M, Chen R, Zhang X, Luo H, Yan C. SLR: a scaffolding algorithm based on long reads and contig classification. BMC Bioinformatics 2019;20:539. [PMID: 31666010 PMCID: PMC6820941 DOI: 10.1186/s12859-019-3114-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 09/23/2019] [Indexed: 11/10/2022]  Open
97
Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. PLoS Comput Biol 2019;15:e1007273. [PMID: 31433799 PMCID: PMC6719893 DOI: 10.1371/journal.pcbi.1007273] [Citation(s) in RCA: 484] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 09/03/2019] [Accepted: 07/18/2019] [Indexed: 12/16/2022]  Open
98
Sedlazeck FJ, Lee H, Darby CA, Schatz MC. Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet 2019;19:329-346. [PMID: 29599501 DOI: 10.1038/s41576-018-0003-4] [Citation(s) in RCA: 320] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
99
Kwan HH, Culibrk L, Taylor GA, Leelakumari S, Tan R, Jackman SD, Tse K, MacLeod T, Cheng D, Chuah E, Kirk H, Pandoh P, Carlsen R, Zhao Y, Mungall AJ, Moore R, Birol I, Marra MA, Rosen DAS, Haulena M, Jones SJM. The Genome of the Steller Sea Lion (Eumetopias jubatus). Genes (Basel) 2019;10:genes10070486. [PMID: 31248052 PMCID: PMC6678222 DOI: 10.3390/genes10070486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 11/16/2022]  Open
100
De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries. Genes (Basel) 2019;10:genes10060426. [PMID: 31163709 PMCID: PMC6627416 DOI: 10.3390/genes10060426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/24/2019] [Accepted: 05/27/2019] [Indexed: 11/16/2022]  Open
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