Towards population-scale long-read sequencing

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works

A global reference for human genetic variation

The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works

Minimap2: Pairwise alignment for nucleotide sequences

Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807 · see citing works

Double-slit photoelectron interference in strong-field ionization of the neon dimer

Kunitski, M., Eicke, N., Huber, P., Köhler, J., Zeller, S., Voigtsberger, J., Schlott, N., Henrichs, K., Sann, H., Trinter, F., et al. (2019) · Institutional Repository of Leibniz Universität Hannover (Leibniz Universität Hannover) · doi:10.15488/5174 · Cited by 8,378 · see citing works

The Ensembl Variant Effect Predictor

McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016) · Genome Biology · doi:10.1186/s13059-016-0974-4 · Cited by 8,099 · see citing works

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., del Angel, G., Levy‐Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., et al. (2013) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1110s43 · Cited by 6,687 · see citing works

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,283 · see citing works

Assembly of long, error-prone reads using repeat graphs

Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986 · see citing works

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021) · Nature Methods · doi:10.1038/s41592-020-01056-5 · Cited by 5,859 · see citing works

Versatile and open software for comparing large genomes

Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254 · see citing works

Coming of age: ten years of next-generation sequencing technologies

Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352 · see citing works

Haplotype-based variant detection from short-read sequencing

Garrison, E., & Marth, G. (2012) · arXiv · doi:10.48550/arxiv.1207.3907 · Cited by 3,700 · see citing works

Performance of neural network basecalling tools for Oxford Nanopore sequencing

Wick, R. R., Judd, L. M., & Holt, K. E. (2019) · Genome Biology · doi:10.1186/s13059-019-1727-y · Cited by 3,221 · see citing works

NanoPack: visualizing and processing long-read sequencing data

De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty149 · Cited by 3,168 · see citing works

Fast and accurate de novo genome assembly from long uncorrected readsPreprint

Vaser, R., Sović, I., Nagarajan, N., & Šikić, M. (2017) · Genome Research · doi:10.1101/gr.214270.116 · Cited by 3,059 · see citing works

ANGSD: Analysis of Next Generation Sequencing Data

Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0356-4 · Cited by 2,982 · see citing works

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

Johnson, J. S., Spakowicz, D. J., Hong, B., Petersen, L., Demkowicz, P. C., Chen, L., Leopold, S. R., Hanson, B., Agresta, H. O., Gerstein, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13036-1 · Cited by 2,286 · see citing works

Nanopore sequencing and assembly of a human genome with ultra-long reads

Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892 · see citing works

cDNA sequence of human apolipoprotein(a) is homologous to plasminogen

McLean, J. W., Tomlinson, J. E., Kuang, W.-J., Eaton, D. L., Chen, E. Y., Fless, G. M., Scanu, A. M., & Lawn, R. M. (1987) · Nature · doi:10.1038/330132a0 · Cited by 1,886 · cited 1× · see citing works

Phased diploid genome assembly with single-molecule real-time sequencing

Chin, C.-S., Peluso, P. S., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O’Malley, R. C., Figueroa-Balderas, R. E., Morales‐Cruz, A., et al. (2016) · Nature Methods · doi:10.1038/nmeth.4035 · Cited by 1,847 · see citing works

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841 · see citing works

A universal SNP and small-indel variant caller using deep neural networks

Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., Newburger, D., Dijamco, J., Nguyen, N., Afshar, P. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4235 · Cited by 1,840 · see citing works

Accurate detection of complex structural variations using single-molecule sequencing

Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., & Schatz, M. C. (2018) · Nature Methods · doi:10.1038/s41592-018-0001-7 · Cited by 1,601 · see citing works

Adaptive seeds tame genomic sequence comparisonPreprint

Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., & Frith, M. C. (2011) · Genome Research · doi:10.1101/gr.113985.110 · Cited by 1,252 · see citing works

Long-read human genome sequencing and its applications

Logsdon, G. A., Vollger, M. R., & Eichler, E. E. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0236-x · Cited by 1,222 · see citing works

Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome

Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F., Kim, P. M., Palejev, D., Carriero, N. J., Du, L., et al. (2007) · Science · doi:10.1126/science.1149504 · Cited by 1,163 · see citing works

metaFlye: scalable long-read metagenome assembly using repeat graphs

Kolmogorov, M., Bickhart, D. M., Behsaz, B., Gurevich, A. A., Rayko, M., Shin, S. B., Kuhn, K. L., Yuan, J., Polevikov, E., Smith, T. P. L., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-00971-x · Cited by 1,087 · see citing works

Pan-Genome of Wild and Cultivated Soybeans

Liu, Y., Du, H., Li, P., Shen, Y., Peng, H., Liu, S., Zhou, G., Zhang, H., Liu, Z., Shi, M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.023 · Cited by 983 · see citing works

Expandable DNA repeats and human disease

Mirkin, S. M. (2007) · Nature · doi:10.1038/nature05977 · Cited by 934 · see citing works

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08148-z · Cited by 891 · see citing works

National Human Genome Research Institute

National Cancer Institute (2020) · Definitions · doi:10.32388/mrapt2 · Cited by 872 · see citing works

Variation graph toolkit improves read mapping by representing genetic variation in the reference

Garrison, E., Sirén, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4227 · Cited by 821 · see citing works

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) · doi:10.1038/ncomms14061 · Cited by 815 · see citing works

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.021 · Cited by 810 · see citing works

Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus

Song, J., Guan, Z., Hu, J., Guo, C., Yang, Z., Wang, S., Liu, D., Wang, B., Lu, S., Zhou, R., et al. (2020) · Nature Plants · doi:10.1038/s41477-019-0577-7 · Cited by 795 · see citing works

Telomere-to-telomere assembly of a complete human X chromosome

Miga, K. H., Koren, S., Rhie, A., Vollger, M. R., Gershman, A., Bzikadze, A., Brooks, S., Howe, E., Porubsky, D., Logsdon, G. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2547-7 · Cited by 765 · see citing works

Structural variant calling: the long and the short of it

Mahmoud, M., Gobet, N., Cruz-Dávalos, D. I., Mounier, N., Dessimoz, C., & Sedlazeck, F. J. (2019) · Genome Biology · doi:10.1186/s13059-019-1828-7 · Cited by 725 · cited 6× · see citing works

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long readsPreprint

Nurk, S., Walenz, B. P., Rhie, A., Vollger, M. R., Logsdon, G. A., Grothe, R., Miga, K. H., Eichler, E. E., Phillippy, A. M., & Koren, S. (2020) · Genome Research · doi:10.1101/gr.263566.120 · Cited by 709 · see citing works

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702 · see citing works

THE AVERAGE NUMBER OF GENERATIONS UNTIL FIXATION OF A MUTANT GENE IN A FINITE POPULATION

Kimura, M., & Ohta, T. (1969) · Genetics · doi:10.1093/genetics/61.3.763 · Cited by 683 · see citing works

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A. J., Qiu, Y., et al. (2021) · Science · doi:10.1126/science.abg5289 · Cited by 681 · see citing works

Structural variation in the sequencing era

Ho, S. S., Urban, A. E., & Mills, R. E. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0180-9 · Cited by 608 · see citing works

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2871-y · Cited by 586 · cited 1× · see citing works

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0503-6 · Cited by 567 · see citing works

Plant pan-genomes are the new reference

Bayer, P. E., Golicz, A. A., Scheben, A., Batley, J., & Edwards, D. (2020) · Nature Plants · doi:10.1038/s41477-020-0733-0 · Cited by 565 · see citing works

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

Sedlazeck, F. J., Lee, H., Darby, C. A., & Schatz, M. C. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0003-4 · Cited by 530 · cited 2× · see citing works

Estimates of Genetic Differentiation Measured by FST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers

Willing, E., Dreyer, C., & van Oosterhout, C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042649 · Cited by 520 · see citing works

Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease

Sone, J., Mitsuhashi, S., Fujita, A., Mizuguchi, T., Hamanaka, K., Mori, K., Koike, H., Hashiguchi, A., Takashima, H., Sugiyama, H., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0459-y · Cited by 498 · see citing works

Characterizing the Major Structural Variant Alleles of the Human Genome

Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.019 · Cited by 492 · see citing works

AnnotSV: an integrated tool for structural variations annotation

Geoffroy, V., Herenger, Y., Kress, A., Stoetzel, C., Piton, A., Dollfus, H., & Muller, J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty304 · Cited by 476 · see citing works

Measures of divergence between populations and the effect of forces that reduce variability

Charlesworth, B. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025953 · Cited by 467 · see citing works

The design and construction of reference pangenome graphs with minigraph

Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455 · see citing works

WhatsHap: fast and accurate read-based phasingPreprint

Martin, M., Patterson, M., Garg, S., Fischer, S. O., Pisanti, N., Klau, G. W., Schönhuth, A., & Marschall, T. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/085050 · Cited by 454 · see citing works

Targeted nanopore sequencing with Cas9-guided adapter ligation

Gilpatrick, T., Lee, I., Graham, J. E., Raimondeau, E., Bowen, R., Heron, A., Downs, B. M., Sukumar, S. V., Sedlazeck, F. J., & Timp, W. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0407-5 · Cited by 432 · see citing works

Long-read-based human genomic structural variation detection with cuteSV

Jiang, T., Liu, Y., Jiang, Y., Li, J., Gao, Y. P., Cui, Z., Liu, B., Liu, B., & Wang, Y. (2020) · Genome biology · doi:10.1186/s13059-020-02107-y · Cited by 424 · see citing works

A robust benchmark for detection of germline large deletions and insertions

Zook, J. M., Hansen, N. F., Olson, N. D., Chapman, L., Mullikin, J. C., Xiao, C., Sherry, S., Koren, S., Phillippy, A. M., Boutros, P. C., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0538-8 · Cited by 418 · see citing works

Readfish enables targeted nanopore sequencing of gigabase-sized genomes

Payne, A., Holmes, N., Clarke, T., Munro, R., Debebe, J., & Loose, M. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-00746-x · Cited by 408 · see citing works

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

Sirén, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., Sibbesen, J. A., Hickey, G., Chang, P.-C., Carroll, A., et al. (2021) · Science · doi:10.1126/science.abg8871 · Cited by 400 · see citing works

SVIM: structural variant identification using mapped long reads

Heller, D., & Vingron, M. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz041 · Cited by 380 · see citing works

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologiesPreprint

Edge, P., Bafna, V., & Bansal, V. (2016) · Genome Research · doi:10.1101/gr.213462.116 · Cited by 379 · see citing works

Assemblytics: a web analytics tool for the detection of variants from an assembly

Nattestad, M., & Schatz, M. C. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw369 · Cited by 376 · see citing works

Discovery and genotyping of structural variation from long-read haploid genome sequence dataPreprint

Huddleston, J., Chaisson, M., Steinberg, K. M., Warren, W., Hoekzema, K., Gordon, D., Graves-Lindsay, T. A., Munson, K. M., Kronenberg, Z. N., Vives, L., et al. (2016) · Genome Research · doi:10.1101/gr.214007.116 · Cited by 376 · see citing works

Pan-genomics in the human genome era

Sherman, R. M., & Salzberg, S. L. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0210-7 · Cited by 364 · see citing works

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

Sherman, R. M., Forman, J., Antonescu, V., Puiu, D., Daya, M., Rafaels, N. M., Boorgula, M. P., Chavan, S., Vergara, C., Ortega, V. E., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0273-y · Cited by 359 · see citing works

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanoporePreprint

Tyson, J. R., James, P. L., Stoddart, D., Sparks, N., Wickenhagen, A., Hall, G., Choi, J. H., Lapointe, H. R., Kamelian, K., Smith, A. D., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.04.283077 · Cited by 356 · see citing works

Genome graphs and the evolution of genome inference

Paten, B., Novak, A. M., Eizenga, J. M., & Garrison, E. (2017) · Genome Research · doi:10.1101/gr.214155.116 · Cited by 351 · see citing works

Computational pan-genomics: status, promises and challenges

Marschall, T., Marz, M., Abeel, T., Dijkstra, L., Dutilh, B. E., Ghaffaari, A., Kersey, P., Kloosterman, W. P., Mäkinen, V., Novak, A. M., et al. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw089 · Cited by 338 · see citing works

The structure, function and evolution of a complete human chromosome 8

Logsdon, G. A., Vollger, M. R., Hsieh, P., Mao, Y., Liskovykh, M. A., Koren, S., Nurk, S., Mercuri, L., Dishuck, P. C., Rhie, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03420-7 · Cited by 326 · see citing works

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) · doi:10.1093/bioinformatics/bty841 · Cited by 326 · see citing works

Genotyping structural variants in pangenome graphs using the vg toolkit

Hickey, G., Heller, D., Monlong, J., Sibbesen, J. A., Sirén, J., Eizenga, J., Dawson, E. T., Garrison, E., Novak, A. M., & Paten, B. (2020) · Genome Biology · doi:10.1186/s13059-020-1941-7 · Cited by 319 · see citing works

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

Shafin, K., Pesout, T., Chang, P.-C., Nattestad, M., Kolesnikov, A., Goel, S., Baid, G., Kolmogorov, M., Eizenga, J. M., Miga, K. H., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01299-w · Cited by 297 · see citing works

Transcriptome variation in human tissues revealed by long-read sequencing

Glinos, D. A., Garborcauskas, G., Hoffman, P. J., Ehsan, N., Jiang, L., Gokden, A., Dai, X.-G., Aguet, F., Brown, K. L., Garimella, K., et al. (2021) · Nature · doi:10.1038/s41586-022-05035-y · Cited by 278 · see citing works

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Ebler, J., Ebert, P., Clarke, W. E., Rausch, T., Audano, P. A., Houwaart, T., Mao, Y., Korbel, J. O., Eichler, E. E., Zody, M. C., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01043-w · Cited by 277 · see citing works

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

Kovaka, S., Fan, Y., Ni, B., Timp, W., & Schatz, M. C. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0731-9 · Cited by 268 · see citing works

Long-read mapping to repetitive reference sequences using Winnowmap2

Jain, C., Rhie, A., Hansen, N. F., Koren, S., & Phillippy, A. M. (2022) · Nature Methods · doi:10.1038/s41592-022-01457-8 · Cited by 266 · see citing works

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits

Beyter, D., Ingimundardóttir, H., Oddsson, Á., Eggertsson, H. P., Björnsson, E., Jónsson, H., Atlason, B. A., Kristmundsdóttir, S., Mehringer, S., Hardarson, M. T., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00865-4 · Cited by 265 · see citing works

Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

Jiao, W., & Schneeberger, K. (2020) · Nature Communications · doi:10.1038/s41467-020-14779-y · Cited by 258 · see citing works

Human Structural Variation: Mechanisms of Chromosome Rearrangements

Weckselblatt, B., & Rudd, M. K. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.05.010 · Cited by 254 · see citing works

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

Edge, P., & Bansal, V. (2019) · Nature Communications · doi:10.1038/s41467-019-12493-y · Cited by 252 · see citing works

GraphAligner: rapid and versatile sequence-to-graph alignment

Rautiainen, M., & Marschall, T. (2020) · Genome Biology · doi:10.1186/s13059-020-02157-2 · Cited by 242 · see citing works

A synthetic-diploid benchmark for accurate variant-calling evaluation

Li, H., Bloom, J. M., Farjoun, Y., Fleharty, M., Gauthier, L. D., Neale, B. M., & MacArthur, D. G. (2018) · Nature Methods · doi:10.1038/s41592-018-0054-7 · Cited by 231 · see citing works

Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines

Cleary, J. G., Braithwaite, R., Gaastra, K., Hilbush, B. S., Inglis, S., Irvine, S. A., Jackson, A., Littin, R., Rathod, M., Ware, D., et al. (2015) · doi:10.1101/023754 · Cited by 230 · see citing works

The presence and impact of reference bias on population genomic studies of prehistoric human populations

Günther, T., & Nettelblad, C. (2019) · PLOS Genetics · doi:10.1371/journal.pgen.1008302 · Cited by 228 · see citing works

Fast and accurate genomic analyses using genome graphs

Rakocevic, G., Semenyuk, V., Lee, W., Spencer, J., Browning, J., Johnson, I. J., Arsenijevic, V., Nadj, J., Ghose, K., Suciu, M., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0316-4 · Cited by 215 · see citing works

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

Lee, I., Razaghi, R., Gilpatrick, T., Molnar, M. M., Gershman, A., Sadowski, N., Sedlazeck, F. J., Hansen, K. D., Simpson, J. T., & Timp, W. (2020) · Nature Methods · doi:10.1038/s41592-020-01000-7 · Cited by 212 · see citing works

Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Tian, L., Jabbari, J. S., Thijssen, R., Gouil, Q. A., Amarasinghe, S. L., Voogd, O., Kariyawasam, H., Du, M. R. M., Schuster, J., Wang, C., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02525-6 · Cited by 207 · see citing works

Long-read sequence and assembly of segmental duplications

Vollger, M. R., Dishuck, P. C., Sorensen, M., Welch, A. E., Dang, V., Dougherty, M. L., Graves-Lindsay, T. A., Wilson, R. K., Chaisson, M., & Eichler, E. E. (2018) · Nature Methods · doi:10.1038/s41592-018-0236-3 · Cited by 204 · see citing works

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Human Genome Structural Variation Consortium, Porubsky, D., Ebert, P., Audano, P. A., Vollger, M. R., Harvey, W. T., Marijon, P., Ebler, J., Munson, K. M., Sorensen, M., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0719-5 · Cited by 203 · see citing works

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

Eggertsson, H. P., Kristmundsdóttir, S., Beyter, D., Jónsson, H., Skúladóttir, Á., Hardarson, M. T., Gudbjartsson, D. F., Stefánsson, K., Halldórsson, B. V., & Melsted, P. (2019) · Nature Communications · doi:10.1038/s41467-019-13341-9 · Cited by 202 · see citing works

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

Olson, N. D., Wagner, J., McDaniel, J., Stephens, S. H., Westreich, S. T., Prasanna, A. G., Johanson, E., Boja, E., Maier, E. J., Serang, O., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100129 · Cited by 202 · see citing works

Benchmarking challenging small variants with linked and long reads

Wagner, J., Olson, N. D., Harris, L. N., McDaniel, J., Khan, Z., Farek, J., Mahmoud, M., Stankovic, A., Kovacevic, V., Yoo, B., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100128 · Cited by 200 · see citing works

Paragraph: a graph-based structural variant genotyper for short-read sequence data

Chen, S., Krusche, P., Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D. R., Schatz, M. C., Sedlazeck, F. J., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1909-7 · Cited by 196 · see citing works

Highly contiguous assemblies of 101 drosophilid genomes

Kim, B. Y., Wang, J., Miller, D. E., Barmina, O. Y., Delaney, E., Thompson, A., Comeault, A. A., Peede, D., D’Agostino, E. R. R., Pelaez, J. N., et al. (2021) · eLife · doi:10.7554/elife.66405 · Cited by 192 · see citing works

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Butler, D., Mozsary, C., Meydan, C., Foox, J., Rosiene, J. A., Shaiber, A., Danko, D., Afshinnekoo, E., MacKay, M. J., Sedlazeck, F. J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21361-7 · Cited by 191 · see citing works

MinIONQC: fast and simple quality control for MinION sequencing data

Lanfear, R., Schalamun, M., Kainer, D., et al. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty654 · Cited by 186 · see citing works

SVIM-asm: structural variant detection from haploid and diploid genome assemblies

Heller, D., & Vingron, M. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1034 · Cited by 183 · see citing works

Chromosome-scale, haplotype-resolved assembly of human genomes

Garg, S., Fungtammasan, A., Carroll, A. W., Chou, M., Schmitt, A. D., Zhou, X., Mac, S., Peluso, P. S., Hatas, E., Ghurye, J., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0711-0 · Cited by 177 · see citing works

Latest techniques to study DNA methylation

Gouil, Q. A., & Keniry, A. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190027 · Cited by 177 · see citing works

Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits

Chakraborty, M., Emerson, J. J., Macdonald, S. J., & Long, A. D. (2019) · Nature Communications · doi:10.1038/s41467-019-12884-1 · Cited by 170 · see citing works

Departure from Hardy Weinberg Equilibrium and Genotyping Error

Chen, B., Cole, J. W., & Grond‐Ginsbach, C. (2017) · Frontiers in Genetics · doi:10.3389/fgene.2017.00167 · Cited by 159 · see citing works

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

English, A. C., Salerno, W. J., & Reid, J. G. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-180 · Cited by 156 · see citing works

Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads

Mitsuhashi, S., Frith, M. C., Mizuguchi, T., Miyatake, S., Toyota, T., Adachi, H., Oma, Y., Kino, Y., Mitsuhashi, H., & Matsumoto, N. (2019) · Genome biology · doi:10.1186/s13059-019-1667-6 · Cited by 155 · see citing works

Genome maps across 26 human populations reveal population-specific patterns of structural variation

Levy‐Sakin, M., Pastor, S. J., Mostovoy, Y., Li, L., Leung, A. K.-Y., McCaffrey, J., YOUNG, E. A., Lam, E. T., Hastie, A. R., Wong, K. H. Y., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08992-7 · Cited by 149 · see citing works

High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

Pootakham, W., Mhuantong, W., Yoocha, T., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-03139-4 · Cited by 144 · see citing works

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

Müller, C. A., Boemo, M. A., Spingardi, P., Kessler, B. M., Kriaučionis, S., Simpson, J. T., & Nieduszynski, C. A. (2019) · Nature Methods · doi:10.1038/s41592-019-0394-y · Cited by 142 · see citing works

How complete are “complete” genome assemblies?—An avian perspective

Peona, V., Weissensteiner, M. H., & Suh, A. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12933 · Cited by 141 · see citing works

Exploring the limit of using a deep neural network on pileup data for germline variant calling

Luo, R., Wong, C.-L., Wong, Y.-S., Tang, C.-I., Liu, C.-M., Leung, C.-M., & Lam, T. (2020) · Nature Machine Intelligence · doi:10.1038/s42256-020-0167-4 · Cited by 138 · see citing works

Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data

Chen, X., Sanchis-Juan, A., French, C. E., Connell, A. J., Delon, I., Kingsbury, Z., Chawla, A., Halpern, A. L., Taft, R. J., Bentley, D. R., et al. (2020) · Genetics in Medicine · doi:10.1038/s41436-020-0754-0 · Cited by 137 · see citing works

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing

Kingan, S. B., Heaton, H., Cudini, J., Lambert, C. C., Baybayan, P. A., Galvin, B. D., Durbin, R. M., Korlach, J., & Lawniczak, M. (2019) · Genes · doi:10.3390/genes10010062 · Cited by 136 · see citing works

Discovery and population genomics of structural variation in a songbird genus

Weissensteiner, M. H., Bunikis, I., Catalán, A., Françoijs, K., Knief, U., Heim, W., Peona, V., Pophaly, S. D., Sedlazeck, F. J., Suh, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17195-4 · Cited by 136 · see citing works

Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome

Maghini, D. G., Moss, E. L., Vance, S. E., & Bhatt, A. S. (2020) · Nature Protocols · doi:10.1038/s41596-020-00424-x · Cited by 128 · see citing works

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

Sevi̇m, V., Lee, J., Egan, R., Clum, A., Hundley, H. N., Lee, J., Everroad, R. C., Detweiler, A. M., Bebout, B. M., Pett‐Ridge, J., et al. (2019) · Scientific Data · doi:10.1038/s41597-019-0287-z · Cited by 127 · see citing works

NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing

Tham, C. Y., Tirado-Magallanes, R., Goh, Y., Fullwood, M. J., Koh, B. T. H., Wang, W., Ng, C. H., Chng, W. J., Thiéry, A. H., Tenen, D. G., et al. (2020) · Genome biology · doi:10.1186/s13059-020-01968-7 · Cited by 126 · see citing works

Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn

Hu, Y., Colantonio, V., Müller, B. S. F., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21380-4 · Cited by 115 · see citing works

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

Schmid, M., Frei, D., Patrignani, A., Schlapbach, R., Frey, J. E., Remus‐Emsermann, M. N. P., & Ahrens, C. H. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky726 · Cited by 107 · see citing works

Evolutionary Genomics of Structural Variation in Asian Rice ( Oryza sativa ) Domestication

Kou, Y., Liao, Y., Toivainen, T., Lv, Y., Tian, X., Emerson, J. J., Gaut, B. S., & Zhou, Y. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa185 · Cited by 105 · see citing works

lra: A long read aligner for sequences and contigs

Ren, J., & Chaisson, M. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009078 · Cited by 105 · see citing works

Newest Methods for Detecting Structural Variations

Coster, W. D., & Broeckhoven, C. V. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.02.003 · Cited by 104 · see citing works

Human Genome Assembly in 100 MinutesPreprint

Chin, C.-S., & Khalak, A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/705616 · Cited by 97 · see citing works

NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Roeck, A. D., Coster, W. D., Bossaerts, L., Cacace, R., Pooter, T. D., Dongen, J. V., D’Hert, S., Rijk, P. D., Stražišar, M., Broeckhoven, C. V., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1856-3 · Cited by 88 · see citing works

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

Leija‐Salazar, M., Sedlazeck, F. J., Toffoli, M., Mullin, S., Mokretar, K., Athanasopoulou, M., Donald, A., Sharma, R., Hughes, D. A., Schapira, A. H. V., et al. (2019) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.564 · Cited by 87 · see citing works

Nanopore‐Based Protein Sequencing Using Biopores: Current Achievements and Open Challenges

Asandei, A., Muccio, G. D., Schiopu, I., et al. (2020) · Small Methods · doi:10.1002/smtd.201900595 · Cited by 86 · see citing works

Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly

Holley, G., Beyter, D., Ingimundardóttir, H., Møller, P. L., Kristmundsdóttir, S., Eggertsson, H. P., & Halldórsson, B. V. (2021) · Genome biology · doi:10.1186/s13059-020-02244-4 · Cited by 82 · see citing works

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

Halvorsen, M., Huh, R., Oskolkov, N., Wen, J., Netotea, S., Giusti‐Rodríguez, P., Karlsson, R., Bryois, J., Nystedt, B., Ameur, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15707-w · Cited by 81 · see citing works

Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

Wu, Z., Jiang, Z., Li, T., Xie, C., Zhao, L., Ouyang, S., Ouyang, S., Liu, Y., Li, T., & Xie, Z. (2021) · Nature Communications · doi:10.1038/s41467-021-26856-x · Cited by 78 · see citing works

Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ

Minkin, I., & Medvedev, P. (2020) · Nature Communications · doi:10.1038/s41467-020-19777-8 · Cited by 77 · see citing works

Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

Chawla, H. S., Lee, H., Gabur, I., Vollrath, P., Tamilselvan‐Nattar‐Amutha, S., Obermeier, C., Schießl, S., Song, J., Liu, K., Guo, L., et al. (2020) · Plant Biotechnology Journal · doi:10.1111/pbi.13456 · Cited by 72 · see citing works

Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

Quan, C., Li, Y., Liu, X., Wang, Y., Ping, J., Lu, Y., & Zhou, G. (2021) · Genome biology · doi:10.1186/s13059-021-02382-3 · Cited by 68 · see citing works

precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regionsPreprint

Olson, N. D., Wagner, J., McDaniel, J., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.13.380741 · Cited by 67 · see citing works

Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders

Hiatt, S. M., Lawlor, J. M. J., Handley, L. H., Ramaker, R. C., Rogers, B. B., Partridge, E. C., Boston, L. B., Williams, M. E., Plott, C., Jenkins, J. W., et al. (2021) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2021.100023 · Cited by 66 · see citing works

Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing

Thibodeau, M. L., O’Neill, K., Dixon, K., Reisle, C., Mungall, K., Krzywinski, M. I., Shen, Y., Lim, H. J., Cheng, D., Tse, K., et al. (2020) · Genetics in Medicine · doi:10.1038/s41436-020-0880-8 · Cited by 65 · see citing works

StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants

Sharo, A. G., Hu, Z., Sunyaev, S. R., & Brenner, S. E. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.12.007 · Cited by 65 · see citing works

Assessing the performance of genome-wide association studies for predicting disease risk

Patron, J., Serra-Cayuela, A., Han, B., Li, C., & Wishart, D. S. (2019) · PLoS ONE · doi:10.1371/journal.pone.0220215 · Cited by 64 · see citing works

A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions

Garg, P., Jadhav, B., Rodriguez, O. L., Patel, N., Martin-Trujillo, A., Jain, M., Metsu, S., Olsen, H. E., Paten, B., Ritz, B. R., et al. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.08.019 · Cited by 63 · see citing works

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system.

Overholt, W., Hölzer, M., Geesink, P., Diezel, C., Marz, M., & Küsel, K. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15186 · Cited by 61 · see citing works

Benchmarking challenging small variants with linked and long readsPreprint

Wagner, J., Olson, N. D., Harris, L. N., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.24.212712 · Cited by 60 · see citing works

Long read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traitsPreprint

Beyter, D., Ingimundardóttir, H., Oddsson, Á., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/848366 · Cited by 60 · see citing works

Incorporating hydrology into climate suitability models changes projections of malaria transmission in Africa

Smith, M. W., Willis, T., Alfieri, L., James, W. H. M., Trigg, M. A., Yamazaki, D., Hardy, A. J., Bisselink, B., De Roo, A., Macklin, M. G., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18239-5 · Cited by 59 · see citing works

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

Ameur, A., Che, H., Martin, M., Bunikis, I., Dahlberg, J., Höijer, I., Häggqvist, S., Vezzi, F., Nordlund, J., Olason, P. I., et al. (2018) · Genes · doi:10.3390/genes9100486 · Cited by 58 · see citing works

Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast

Tusso, S., Nieuwenhuis, B. P. S., Sedlazeck, F. J., Davey, J. W., Jeffares, D. C., & Wolf, J. B. W. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz126 · Cited by 53 · see citing works

Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing

Peto, L., Rodger, G., Carter, D. P., et al. (2021) · Journal of Clinical Microbiology · doi:10.1128/jcm.03271-20 · Cited by 51 · see citing works

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants

Belyeu, J. R., Nicholas, T. J., Pedersen, B. S., Sasani, T. A., Havrilla, J. M., Kravitz, S. N., Conway, M. E., Lohman, B. K., Quinlan, A. R., & Layer, R. M. (2018) · GigaScience · doi:10.1093/gigascience/giy064 · Cited by 46 · see citing works

Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals

Doddapaneni, H., Cregeen, S. J., Sucgang, R., Meng, Q., Qin, X., Avadhanula, V., Chao, H., Menon, V. K., Nicholson, E. G., Henke, D., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0244468 · Cited by 44 · see citing works

Functional annotation of rare structural variation in the human brain

Han, L., Zhao, X., Benton, M. L., Perumal, T. M., Collins, R. L., Hoffman, G. E., Johnson, J., Sloofman, L. G., Wang, H. Z., Stone, M. R., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16736-1 · Cited by 43 · see citing works

Local adaptation and archaic introgression shape global diversity at human structural variant loci

Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., & McCoy, R. C. (2021) · eLife · doi:10.7554/elife.67615 · Cited by 42 · see citing works

Evaluation of computational genotyping of structural variation for clinical diagnoses

Chander, V., Gibbs, R. A., & Sedlazeck, F. J. (2019) · GigaScience · doi:10.1093/gigascience/giz110 · Cited by 39 · see citing works

Regional sequence expansion or collapse in heterozygous genome assemblies

Asalone, K. C., Ryan, K., Yamadi, M., Cohen, A., Farmer, W. G., George, D. J., Joppert, C., Kim, K., Mughal, M. F., Said, R., et al. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008104 · Cited by 36 · see citing works

A pipeline for complete characterization of complex germline rearrangements from long DNA reads

Mitsuhashi, S., Ohori, S., Katoh, K., Frith, M. C., & Matsumoto, N. (2020) · Genome Medicine · doi:10.1186/s13073-020-00762-1 · Cited by 35 · see citing works

Transcriptome variation in human tissues revealed by long-read sequencingPreprint

Glinos, D. A., Garborcauskas, G., Hoffman, P., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.22.427687 · Cited by 34 · see citing works

Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencingPreprint

Tian, L., Jabbari, J. S., Thijssen, R., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.10.243543 · Cited by 33 · see citing works

A long read mapping method for highly repetitive reference sequencesPreprint

Jain, C., Rhie, A., Hansen, N. F., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.01.363887 · Cited by 33 · see citing works

Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networksPreprint

Shafin, K., Pesout, T., Chang, P.-C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.04.433952 · Cited by 33 · see citing works

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomesPreprint

Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.14.426684 · Cited by 30 · see citing works

Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkitPreprint

Sirén, J., Monlong, J., Chang, X. H., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.04.412486 · Cited by 29 · see citing works

TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data

Bolognini, D., Magi, A., Beneš, V., Korbel, J. O., & Rausch, T. (2020) · GigaScience · doi:10.1093/gigascience/giaa101 · Cited by 27 · see citing works

Pangenome-based genome inferencePreprint

Ebler, J., Clarke, W. E., Rausch, T., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.11.378133 · Cited by 25 · see citing works

Linked‐read sequencing enables haplotype‐resolved resequencing at population scale

Lutgen, D., Ritter, R., Olsen, R., Schielzeth, H., Gruselius, J., Ewels, P., García, J. T., Shirihai, H., Schweizer, M., Suh, A., et al. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13192 · Cited by 24 · see citing works

Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencingPreprint

Peto, L., Rodger, G., Carter, D. P., et al. (2020) · medRxiv · doi:10.1101/2020.09.18.20195370 · Cited by 20 · see citing works

Highly contiguous assemblies of 101 drosophilid genomesPreprint

Kim, B. Y., Wang, J., Miller, D. E., Barmina, O. Y., Delaney, E., Thompson, A., Comeault, A. A., Peede, D., D’Agostino, E. R. R., Pelaez, J. N., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.14.422775 · Cited by 19 · see citing works

SVJedi: genotyping structural variations with long reads

Lecompte, L., Peterlongo, P., Lavenier, D. D., & Lemaitre, C. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa527 · Cited by 18 · see citing works

Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individualsPreprint

Doddapaneni, H., Cregeen, S. J., Sucgang, R., Meng, Q., Qin, X., Avadhanula, V., Chao, H., Menon, V. K., Nicholson, E. G., Henke, D. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.27.223495 · Cited by 18 · see citing works

SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencingPreprint

Heller, D., Vingron, M., Church, G. M., Li, H., & Garg, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.25.964445 · Cited by 14 · see citing works

PhaseME: Automatic rapid assessment of phasing quality and phasing improvement

Majidian, S., & Sedlazeck, F. J. (2020) · GigaScience · doi:10.1093/gigascience/giaa078 · Cited by 14 · see citing works

Structural variants in Chinese population and their impact on phenotypes, diseases and population adaptationPreprint

Wu, Z., Jiang, Z., Li, T., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.09.430378 · Cited by 11 · see citing works

Long-read genome sequencing for the diagnosis of neurodevelopmental disordersPreprint

Hiatt, S. M., Lawlor, J. M. J., Handley, L. H., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.02.185447 · Cited by 10 · see citing works

Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data

Chiara, M., Zambelli, F., Picardi, E., Horner, D. S., & Pesole, G. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz099 · Cited by 10 · see citing works

StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variantsPreprint

Sharo, A. G., Hu, Z., Sunyaev, S. R., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.15.097048 · Cited by 10 · see citing works

lra: the Long Read Aligner for Sequences and ContigsPreprint

Ren, J., & Chaisson, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.15.383273 · Cited by 10 · see citing works

Optimized sample selection for cost-efficient long-read population sequencingPreprint

Ranallo-Benavidez, T. R., Lemmon, Z. H., Soyk, S., Aganezov, S. S., Salerno, W. J., McCoy, R. C., Lippman, Z. B., Schatz, M. C., & Sedlazeck, F. J. (2021) · Genome Research · doi:10.1101/gr.264879.120 · Cited by 10 · see citing works

Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variantsPreprint

Miller, D. E., Sulovari, A., Wang, T., Loucks, H., Hoekzema, K., Munson, K. M., Lewis, A. P., Fuerte, E. P. A., Paschal, C. R., Thies, J. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.03.365395 · Cited by 9 · see citing works

Functional annotation of rare structural variation in the human brainPreprint

Han, L., Zhao, X., Benton, M. L., Perumal, T. M., Collins, R. L., Hoffman, G. E., Johnson, J., Sloofman, L. G., Wang, H. Z., Brennand, K., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/711754 · Cited by 8 · see citing works

Long read metagenomics, the next step?Preprint

Haro-Moreno, J. M., López‐Pérez, M., & Rodríguez‐Valera, F. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.11.378109 · Cited by 8 · see citing works

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Fatima, N., Petri, A., Gyllensten, U. B., Feuk, L., & Ameur, A. (2020) · Genes · doi:10.3390/genes11121444 · Cited by 7 · see citing works

Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy

Chandak, S., Tatwawadi, K., Sridhar, S., & Weissman, T. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1017 · Cited by 7 · see citing works

Correction: Long-read trio sequencing of individuals with unsolved intellectual disability

Pauper, M., Küçük, E., Wenger, A. M., et al. (2021) · European Journal of Human Genetics · doi:10.1038/s41431-021-00868-z · Cited by 5 · see citing works

Characterization of Structural Variation in Tibetans Reveals New Evidence of High-altitude Adaptation and IntrogressionPreprint

Quan, C., Li, Y., Wang, Y., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.01.401174 · Cited by 4 · see citing works

Imputed Genomic Data Reveals a Moderate Effect of Low Frequency Variants to the Heritability of Complex Human TraitsPreprint

Hartman, K., Rashkin, S. R., Witte, J. S., & Hernandez, R. D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2019.12.18.879916 · Cited by 4 · see citing works

Long-read sequencing resolves structural variants in SERPINC1 causing antithrombin deficiency and identifies a complex rearrangement and a retrotransposon insertion not characterized by routine diagnostic methodsPreprint

de la Morena‐Barrio, B., Stephens, J. C., de la Morena‐Barrio, M. E., Stefanucci, L., Padilla, J., Miñano, A., Gleadall, N., Garcı́a, J. L., Fernández, M. F. L., Morange, P., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.28.271932 · Cited by 3 · see citing works

Local adaptation and archaic introgression shape global diversity at human structural variant lociPreprint

Yan, S. M., Sherman, R. M., Taylor, D. J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.26.428314 · Cited by 2 · see citing works

Curated variation benchmarks for challenging medically relevant autosomal genes

Wagner, J., Olson, N. D., Harris, L., McDaniel, J., Cheng, H., Fungtammasan, A., Hwang, Y.-C., Gupta, R., Wenger, A. M., Rowell, W. J., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01158-1 · Cited by 241 · see citing works

Comprehensive genome analysis and variant detection at scale using DRAGEN

Behera, S., Catreux, S., Rossi, M., Truong, S., Huang, Z., Ruehle, M., Visvanath, A., Parnaby, G., Roddey, C., Onuchic, V., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02382-1 · Cited by 137 · see citing works

Structural variation across 138,134 samples in the TOPMed consortium

Jun, G., English, A., Metcalf, G., Yang, J., Chaisson, M., Pankratz, N., Menon, V., Salerno, W., Krasheninina, O., Smith, A., et al. (2023) · doi:10.21203/rs.3.rs-2515453/v1 · Cited by 24 · see citing works

DETERMINING QUALITY REQUIREMENTS AT THE UNIVERSITIES TO IMPROVE THE QUALITY OF EDUCATION

Mustafa, N. H., Kelesbayev, D., & Alibekova, Z. D. (2018) · The Journal of Economic Research & Business Administration · doi:10.26577/be-2018-2-2141

Population and Sample

Sahu, P. K. (2016) · Springer eBooks · doi:10.1007/978-81-322-2831-8_5 · Cited by 2 · see citing works

유전 및 육종 : 한우의 6개월령 및 12개월령 체중의 유전적 변화에 대한 모의실험

안병석, 김내수, 주종철, et al. (1996)

Review of scale-to-scale changes between the 2016–2018 scale and the 2019–2021 scale, calculated using the 2016–2018 scale methodology

(2019) · Report of the Committee on Contributions, United Nations · doi:10.18356/9da610c7-en

Review of scale-to-scale changes between the 2013-2015 scale and the 2016-2018 scale, calculated using the 2013-2015 scale methodology

(2016) · Report of the Committee on Contributions, United Nations · doi:10.18356/400b84d4-en