Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, et al.Mapping and characterization of structural variation in 17,795 human genomes. Nature. 2020; 583(7814):83–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
UK, 10K consortium, et al.The uk10k project identifies rare variants in health and disease. Nature. 2015; 526(7571):82.
Article
Google Scholar
Merker JD, Wenger AM, Sneddon T, Grove M, Zappala Z, Fresard L, Waggott D, Utiramerur S, Hou Y, Smith KS, et al.Long-read genome sequencing identifies causal structural variation in a mendelian disease. Genet Med. 2018; 20(1):159–63.
Article
CAS
PubMed
Google Scholar
Sanchis-Juan A, Stephens J, French CE, Gleadall N, Mégy K, Penkett C, Shamardina O, Stirrups K, Delon I, Dewhurst E, et al.Complex structural variants in mendelian disorders: identification and breakpoint resolution using short-and long-read genome sequencing. Genome Med. 2018; 10(1):1–10.
Article
Google Scholar
Jiang Y. -h., Yuen RK, Jin X, Wang M, Chen N, Wu X, Ju J, Mei J, Shi Y, He M, et al.Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. Am J Hum Genet. 2013; 93(2):249–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Niemi ME, Martin HC, Rice DL, Gallone G, Gordon S, Kelemen M, McAloney K, McRae J, Radford EJ, Yu S, et al.Common genetic variants contribute to risk of rare severe neurodevelopmental disorders. Nature. 2018; 562(7726):268–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Macintyre G, Ylstra B, Brenton JD. Sequencing structural variants in cancer for precision therapeutics. Trends Genet. 2016; 32(9):530–42.
Article
CAS
PubMed
Google Scholar
Zhao X, Collins RL, Lee W-P, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, et al.Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. Am J Hum Genet. 2021; 108(5):919–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, Von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018; 15(6):461–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huddleston J, Chaisson MJ, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, et al.Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res. 2017; 27(5):677–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stancu MC, Van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, De Ligt J, Pregno G, Giachino D, Mandrile G, Valle-Inclan JE, et al.Mapping and phasing of structural variation in patient genomes using nanopore sequencing. Nat Commun. 2017; 8(1):1–13.
Article
Google Scholar
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, et al.Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science. 2021; 372(6537):7117.
Article
Google Scholar
Mahmoud M, Gobet N, Cruz-Dávalos DI, Mounier N, Dessimoz C, Sedlazeck FJ. Structural variant calling: the long and the short of it. Genome Biol. 2019; 20(1):246.
Article
PubMed
PubMed Central
Google Scholar
Chen S, Krusche P, Dolzhenko E, Sherman RM, Petrovski R, Schlesinger F, Kirsche M, Bentley DR, Schatz MC, Sedlazeck FJ, et al.Paragraph: a graph-based structural variant genotyper for short-read sequence data. Genome Biol. 2019; 20(1):1–13.
Article
Google Scholar
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, et al.Real-time dna sequencing from single polymerase molecules. Science. 2009; 323(5910):133–8.
Article
CAS
PubMed
Google Scholar
Clarke J, Wu H-C, Jayasinghe L, Patel A, Reid S, Bayley H. Continuous base identification for single-molecule nanopore dna sequencing. Nature Nanotechnol. 2009; 4(4):265–70.
Article
CAS
Google Scholar
Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H, et al.A structural variation reference for medical and population genetics. Nature. 2020; 581(7809):444–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Layer RM, Chiang C, Quinlan AR, Hall IM. Lumpy: a probabilistic framework for structural variant discovery. Genome Biol. 2014; 15(6):84.
Article
Google Scholar
Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. Delly: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012; 28(18):333–9.
Article
Google Scholar
Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Källberg M, Cox AJ, Kruglyak S, Saunders CT. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016; 32(8):1220–2.
Article
CAS
PubMed
Google Scholar
Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, et al.A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnol. 2020; 38(11):1347–55.
Article
CAS
Google Scholar
Parikh H, Mohiyuddin M, Lam HY, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, et al.svclassify: a method to establish benchmark structural variant calls. BMC Genomics. 2016; 17(1):64.
Article
PubMed
PubMed Central
Google Scholar
Chaisson MJ, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, et al.Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun. 2019; 10(1):1–16.
Article
CAS
Google Scholar
Chin C-S, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautiainen M, Aganezov S, Kirsche M, Zarate S, et al.A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nat Commun. 2020; 11(1):1–9.
Article
Google Scholar
English AC, Salerno WJ, Hampton OA, Gonzaga-Jauregui C, Ambreth S, Ritter DI, Beck CR, Davis CF, Dahdouli M, Ma S, et al.Assessing structural variation in a personal genomeŮtowards a human reference diploid genome. BMC Genomics. 2015; 16(1):286.
Article
PubMed
PubMed Central
Google Scholar
Cheng H, Concepcion GT, Feng X, Zhang H, Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods. 2021; 18(2):170–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao X, Weber AM, Mills RE. A recurrence-based approach for validating structural variation using long-read sequencing technology. GigaScience. 2017; 6(8):061.
Article
Google Scholar
Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D. A synthetic-diploid benchmark for accurate variant-calling evaluation. Nat Methods. 2018; 15(8):595–7.
Article
PubMed
PubMed Central
Google Scholar
Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M. Wham: identifying structural variants of biological consequence. PLoS Comput Biol. 2015; 11(12):1004572.
Article
Google Scholar
Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, et al.Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019; 37(10):1155–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34(18):3094–100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nature Biotechnol. 2011; 29(1):24–6.
Article
CAS
Google Scholar
Ren J, Chaisson MJ. lra: A long read aligner for sequences and contigs. PLOS Comput Biol. 2021; 17(6):1009078.
Article
Google Scholar
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH-Y, et al.An integrated map of structural variation in 2,504 human genomes. Nature. 2015; 526(7571):75–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR, Layer RM. Samplot: a platform for structural variant visual validation and automated filtering. Genome Biol. 2021; 22(1):1–13.
Article
Google Scholar
Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, et al.Segmental duplications and copy-number variation in the human genome. Am J Hum Genet. 2005; 77(1):78–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin J, Yang X, Kosters W, Xu T, Jia Y, Wang S, Zhu Q, Ryan M, Guo L, Zhang C, Lee C, Devinel SE, Eichler EE, Ye K. Mako: A graph-based pattern growth approach to detect complex structural variants. Genomics Proteomics Bioinforma. 2021. https://doi.org/10.1016/j.gpb.2021.03.007.
Yang J, Chaisson MJ. TT-Mars: structural variants assessment based on haplotype-resolved assemblies. GitHub. 2022. https://github.com/ChaissonLab/TT-Mars.git. Accessed 23 Mar 2022.
Yang J, Chaisson MJ. TT-Mars: structural variants assessment based on haplotype-resolved assemblies. Zenodo. 2022. https://doi.org/10.5281/zenodo.6380880.