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5. FixItFelix: improving genomic analysis by fixing reference errors

Author

Behera, Sairam, LeFaive, Jonathon, Orchard, Peter, Mahmoud, Medhat, Paulin, Luis F, Farek, Jesse, Soto, Daniela C, Parker, Stephen CJ, Smith, Albert V, Dennis, Megan Y, Zook, Justin M, and Sedlazeck, Fritz J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Mental health, Humans, Genomics, Genome, Human, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Reference, GRCh38, T2T-CHM13, Variant, SNV, INDEL, Medically relevant genes, Remapping, GIAB, eQTL, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical relevance. Here, we present FixItFelix, an efficient remapping approach, together with a modified version of the GRCh38 reference genome that improves the subsequent analysis across these genes within minutes for an existing alignment file while maintaining the same coordinates. We showcase these improvements over multi-ethnic control samples, demonstrating improvements for population variant calling as well as eQTL studies.

Published
2023

6. Semi-automated assembly of high-quality diploid human reference genomes

Author

Jarvis, Erich D, Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R, Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A, Carnevali, Paolo, Chaisson, Mark JP, Chin, Chen-Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S, Fulton, Lucinda L, Garg, Shilpa, Gerton, Jennifer L, Ghurye, Jay, Granat, Anastasiya, Green, Richard E, Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B, Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O, Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W, McDaniel, Jennifer, Nie, Fan, Olsen, Hugh E, Olson, Nathan D, Pesout, Trevor, Potapova, Tamara, Puiu, Daniela, Regier, Allison, Ruan, Jue, Salzberg, Steven L, Sanders, Ashley D, Schatz, Michael C, Schmitt, Anthony, Schneider, Valerie A, Selvaraj, Siddarth, Shafin, Kishwar, Shumate, Alaina, Stitziel, Nathan O, Stober, Catherine, Torrance, James, Wagner, Justin, Wang, Jianxin, Wenger, Aaron, Xiao, Chuanle, Zimin, Aleksey V, Zhang, Guojie, Wang, Ting, Li, Heng, Garrison, Erik, Haussler, David, Hall, Ira, Zook, Justin M, Eichler, Evan E, Phillippy, Adam M, Paten, Benedict, Howe, Kerstin, and Miga, Karen H

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Humans, Chromosome Mapping, Diploidy, Genome, Human, Haplotypes, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Reference Standards, Genomics, Chromosomes, Human, Genetic Variation, Human Pangenome Reference Consortium, General Science & Technology
Abstract

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

Published
2022

7. The complete sequence of a human Y chromosome

Author

Rhie, Arang, Nurk, Sergey, Cechova, Monika, Hoyt, Savannah J., Taylor, Dylan J., Altemose, Nicolas, Hook, Paul W., Koren, Sergey, Rautiainen, Mikko, Alexandrov, Ivan A., Allen, Jamie, Asri, Mobin, Bzikadze, Andrey V., Chen, Nae-Chyun, Chin, Chen-Shan, Diekhans, Mark, Flicek, Paul, Formenti, Giulio, Fungtammasan, Arkarachai, Garcia Giron, Carlos, Garrison, Erik, Gershman, Ariel, Gerton, Jennifer L., Grady, Patrick G. S., Guarracino, Andrea, Haggerty, Leanne, Halabian, Reza, Hansen, Nancy F., Harris, Robert, Hartley, Gabrielle A., Harvey, William T., Haukness, Marina, Heinz, Jakob, Hourlier, Thibaut, Hubley, Robert M., Hunt, Sarah E., Hwang, Stephen, Jain, Miten, Kesharwani, Rupesh K., Lewis, Alexandra P., Li, Heng, Logsdon, Glennis A., Lucas, Julian K., Makalowski, Wojciech, Markovic, Christopher, Martin, Fergal J., Mc Cartney, Ann M., McCoy, Rajiv C., McDaniel, Jennifer, McNulty, Brandy M., Medvedev, Paul, Mikheenko, Alla, Munson, Katherine M., Murphy, Terence D., Olsen, Hugh E., Olson, Nathan D., Paulin, Luis F., Porubsky, David, Potapova, Tamara, Ryabov, Fedor, Salzberg, Steven L., Sauria, Michael E. G., Sedlazeck, Fritz J., Shafin, Kishwar, Shepelev, Valery A., Shumate, Alaina, Storer, Jessica M., Surapaneni, Likhitha, Taravella Oill, Angela M., Thibaud-Nissen, Françoise, Timp, Winston, Tomaszkiewicz, Marta, Vollger, Mitchell R., Walenz, Brian P., Watwood, Allison C., Weissensteiner, Matthias H., Wenger, Aaron M., Wilson, Melissa A., Zarate, Samantha, Zhu, Yiming, Zook, Justin M., Eichler, Evan E., O’Neill, Rachel J., Schatz, Michael C., Miga, Karen H., Makova, Kateryna D., and Phillippy, Adam M.

Published
2023
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8. A complete reference genome improves analysis of human genetic variation

Author

Aganezov, Sergey, Yan, Stephanie M, Soto, Daniela C, Kirsche, Melanie, Zarate, Samantha, Avdeyev, Pavel, Taylor, Dylan J, Shafin, Kishwar, Shumate, Alaina, Xiao, Chunlin, Wagner, Justin, McDaniel, Jennifer, Olson, Nathan D, Sauria, Michael EG, Vollger, Mitchell R, Rhie, Arang, Meredith, Melissa, Martin, Skylar, Lee, Joyce, Koren, Sergey, Rosenfeld, Jeffrey A, Paten, Benedict, Layer, Ryan, Chin, Chen-Shan, Sedlazeck, Fritz J, Hansen, Nancy F, Miller, Danny E, Phillippy, Adam M, Miga, Karen H, McCoy, Rajiv C, Dennis, Megan Y, Zook, Justin M, and Schatz, Michael C

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Generic health relevance, Genetic Variation, Genome, Human, Genomics, Humans, Reference Standards, Sequence Analysis, DNA, General Science & Technology
Abstract

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.

Published
2022

9. Complete genomic and epigenetic maps of human centromeres

Author

Altemose, Nicolas, Logsdon, Glennis A, Bzikadze, Andrey V, Sidhwani, Pragya, Langley, Sasha A, Caldas, Gina V, Hoyt, Savannah J, Uralsky, Lev, Ryabov, Fedor D, Shew, Colin J, Sauria, Michael EG, Borchers, Matthew, Gershman, Ariel, Mikheenko, Alla, Shepelev, Valery A, Dvorkina, Tatiana, Kunyavskaya, Olga, Vollger, Mitchell R, Rhie, Arang, McCartney, Ann M, Asri, Mobin, Lorig-Roach, Ryan, Shafin, Kishwar, Lucas, Julian K, Aganezov, Sergey, Olson, Daniel, de Lima, Leonardo Gomes, Potapova, Tamara, Hartley, Gabrielle A, Haukness, Marina, Kerpedjiev, Peter, Gusev, Fedor, Tigyi, Kristof, Brooks, Shelise, Young, Alice, Nurk, Sergey, Koren, Sergey, Salama, Sofie R, Paten, Benedict, Rogaev, Evgeny I, Streets, Aaron, Karpen, Gary H, Dernburg, Abby F, Sullivan, Beth A, Straight, Aaron F, Wheeler, Travis J, Gerton, Jennifer L, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Dennis, Megan Y, O'Neill, Rachel J, Zook, Justin M, Schatz, Michael C, Pevzner, Pavel A, Diekhans, Mark, Langley, Charles H, Alexandrov, Ivan A, and Miga, Karen H

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Centromere, Chromosome Mapping, Epigenesis, Genetic, Evolution, Molecular, Genome, Human, Genomics, Humans, Repetitive Sequences, Nucleic Acid, General Science & Technology
Abstract

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.

Published
2022

10. The complete sequence of a human genome

Author

Nurk, Sergey, Koren, Sergey, Rhie, Arang, Rautiainen, Mikko, Bzikadze, Andrey V, Mikheenko, Alla, Vollger, Mitchell R, Altemose, Nicolas, Uralsky, Lev, Gershman, Ariel, Aganezov, Sergey, Hoyt, Savannah J, Diekhans, Mark, Logsdon, Glennis A, Alonge, Michael, Antonarakis, Stylianos E, Borchers, Matthew, Bouffard, Gerard G, Brooks, Shelise Y, Caldas, Gina V, Chen, Nae-Chyun, Cheng, Haoyu, Chin, Chen-Shan, Chow, William, de Lima, Leonardo G, Dishuck, Philip C, Durbin, Richard, Dvorkina, Tatiana, Fiddes, Ian T, Formenti, Giulio, Fulton, Robert S, Fungtammasan, Arkarachai, Garrison, Erik, Grady, Patrick GS, Graves-Lindsay, Tina A, Hall, Ira M, Hansen, Nancy F, Hartley, Gabrielle A, Haukness, Marina, Howe, Kerstin, Hunkapiller, Michael W, Jain, Chirag, Jain, Miten, Jarvis, Erich D, Kerpedjiev, Peter, Kirsche, Melanie, Kolmogorov, Mikhail, Korlach, Jonas, Kremitzki, Milinn, Li, Heng, Maduro, Valerie V, Marschall, Tobias, McCartney, Ann M, McDaniel, Jennifer, Miller, Danny E, Mullikin, James C, Myers, Eugene W, Olson, Nathan D, Paten, Benedict, Peluso, Paul, Pevzner, Pavel A, Porubsky, David, Potapova, Tamara, Rogaev, Evgeny I, Rosenfeld, Jeffrey A, Salzberg, Steven L, Schneider, Valerie A, Sedlazeck, Fritz J, Shafin, Kishwar, Shew, Colin J, Shumate, Alaina, Sims, Ying, Smit, Arian FA, Soto, Daniela C, Sović, Ivan, Storer, Jessica M, Streets, Aaron, Sullivan, Beth A, Thibaud-Nissen, Françoise, Torrance, James, Wagner, Justin, Walenz, Brian P, Wenger, Aaron, Wood, Jonathan MD, Xiao, Chunlin, Yan, Stephanie M, Young, Alice C, Zarate, Samantha, Surti, Urvashi, McCoy, Rajiv C, Dennis, Megan Y, Alexandrov, Ivan A, Gerton, Jennifer L, O’Neill, Rachel J, Timp, Winston, Zook, Justin M, Schatz, Michael C, Eichler, Evan E, Miga, Karen H, and Phillippy, Adam M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Generic health relevance, Cell Line, Chromosomes, Artificial, Bacterial, Chromosomes, Human, Genome, Human, Human Genome Project, Humans, Reference Values, Sequence Analysis, DNA, General Science & Technology
Abstract

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Published
2022

11. A draft human pangenome reference

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cook-Deegan, Robert M., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kenny, Eimear E., Koenig, Barbara A., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M. D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J. P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Jarvis, Erich D., Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, and Paten, Benedict

Published
2023
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12. A robust benchmark for detection of germline large deletions and insertions

Author

Zook, Justin M, Hansen, Nancy F, Olson, Nathan D, Chapman, Lesley, Mullikin, James C, Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M, Boutros, Paul C, Sahraeian, Sayed Mohammad E, Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E, Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T, Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L, Bashir, Ali, Jackman, Shaun, Farrell, John J, Wenger, Aaron M, Alkan, Can, Soylev, Arda, Schatz, Michael C, Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C, Rosenfeld, Jeffrey A, Zhou, Weichen, Mills, Ryan E, Sage, Jay M, Davis, Jennifer R, Kaiser, Michael D, Oliver, John S, Catalano, Anthony P, Chaisson, Mark JP, Spies, Noah, Sedlazeck, Fritz J, and Salit, Marc

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Diploidy, Genomic Structural Variation, Germ-Line Mutation, Humans, INDEL Mutation, Molecular Sequence Annotation, Sequence Analysis, DNA
Abstract

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.

Published
2020

13. Author Correction: A robust benchmark for detection of germline large deletions and insertions

Author

Zook, Justin M, Hansen, Nancy F, Olson, Nathan D, Chapman, Lesley, Mullikin, James C, Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M, Boutros, Paul C, Sahraeian, Sayed Mohammad E, Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E, Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T, Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L, Bashir, Ali, Jackman, Shaun, Farrell, John J, Wenger, Aaron M, Alkan, Can, Soylev, Arda, Schatz, Michael C, Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C, Rosenfeld, Jeffrey A, Zhou, Weichen, Mills, Ryan E, Sage, Jay M, Davis, Jennifer R, Kaiser, Michael D, Oliver, John S, Catalano, Anthony P, Chaisson, Mark JP, Spies, Noah, Sedlazeck, Fritz J, and Salit, Marc

Subjects
Control Engineering, Mechatronics and Robotics, Engineering
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

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

Author

Shafin, Kishwar, Pesout, Trevor, Lorig-Roach, Ryan, Haukness, Marina, Olsen, Hugh E, Bosworth, Colleen, Armstrong, Joel, Tigyi, Kristof, Maurer, Nicholas, Koren, Sergey, Sedlazeck, Fritz J, Marschall, Tobias, Mayes, Simon, Costa, Vania, Zook, Justin M, Liu, Kelvin J, Kilburn, Duncan, Sorensen, Melanie, Munson, Katy M, Vollger, Mitchell R, Monlong, Jean, Garrison, Erik, Eichler, Evan E, Salama, Sofie, Haussler, David, Green, Richard E, Akeson, Mark, Phillippy, Adam, Miga, Karen H, Carnevali, Paolo, Jain, Miten, and Paten, Benedict

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Bioengineering, Human Genome, Nanotechnology, Generic health relevance, Algorithms, Benchmarking, Chromosomes, Human, Deep Learning, Genome, Human, Genomics, HLA Antigens, Haploidy, High-Throughput Nucleotide Sequencing, Humans, Nanopore Sequencing, Sequence Analysis, DNA
Abstract

De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish and HELEN. Using a single PromethION nanopore sequencer and our toolkit, we assembled 11 highly contiguous human genomes de novo in 9 d. We achieved roughly 63× coverage, 42-kb read N50 values and 6.5× coverage in reads >100 kb using three flow cells per sample. Shasta produced a complete haploid human genome assembly in under 6 h on a single commercial compute node. MarginPolish and HELEN polished haploid assemblies to more than 99.9% identity (Phred quality score QV = 30) with nanopore reads alone. Addition of proximity-ligation sequencing enabled near chromosome-level scaffolds for all 11 genomes. We compare our assembly performance to existing methods for diploid, haploid and trio-binned human samples and report superior accuracy and speed.

Published
2020

15. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Olson, Nathan D., Puiu, Daniela, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sirén, Jouni, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M.D., Zimin, Aleksey V., Popejoy, Alice B., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Jarvis, Erich D., Miga, Karen H., Wang, Ting, Garrison, Erik, Marschall, Tobias, Hall, Ira, Li, Heng, Paten, Benedict, Greer, Stephanie U., Pavlichin, Dmitri S., Zhou, Bo, Urban, Alexander E., and Weissman, Tsachy

Published
2023
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17. Best practices for benchmarking germline small-variant calls in human genomes

Author

Krusche, Peter, Trigg, Len, Boutros, Paul C, Mason, Christopher E, De La Vega, Francisco M, Moore, Benjamin L, Gonzalez-Porta, Mar, Eberle, Michael A, Tezak, Zivana, Lababidi, Samir, Truty, Rebecca, Asimenos, George, Funke, Birgit, Fleharty, Mark, Chapman, Brad A, Salit, Marc, and Zook, Justin M

Subjects
Biological Sciences, Genetics, Clinical Research, Human Genome, Generic health relevance, Algorithms, Benchmarking, Exome, Genome, Human, Genomics, Germ Cells, High-Throughput Nucleotide Sequencing, Humans, Polymorphism, Single Nucleotide, Software, Global Alliance for Genomics and Health Benchmarking Team
Abstract

Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant-calling tools and the metrics used to assess their performance continue to improve, important challenges remain. Here, as part of the Global Alliance for Genomics and Health (GA4GH), we present a benchmarking framework for variant calling. We provide guidance on how to match variant calls with different representations, define standard performance metrics, and stratify performance by variant type and genome context. We describe limitations of high-confidence calls and regions that can be used as truth sets (for example, single-nucleotide variant concordance of two methods is 99.7% inside versus 76.5% outside high-confidence regions). Our web-based app enables comparison of variant calls against truth sets to obtain a standardized performance report. Our approach has been piloted in the PrecisionFDA variant-calling challenges to identify the best-in-class variant-calling methods within high-confidence regions. Finally, we recommend a set of best practices for using our tools and evaluating the results.

Published
2019

18. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Author

Mc Cartney, Ann M., Shafin, Kishwar, Alonge, Michael, Bzikadze, Andrey V., Formenti, Giulio, Fungtammasan, Arkarachai, Howe, Kerstin, Jain, Chirag, Koren, Sergey, Logsdon, Glennis A., Miga, Karen H., Mikheenko, Alla, Paten, Benedict, Shumate, Alaina, Soto, Daniela C., Sović, Ivan, Wood, Jonathan M. D., Zook, Justin M., Phillippy, Adam M., and Rhie, Arang

Published
2022
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19. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

Author

Olson, Nathan D., Wagner, Justin, McDaniel, Jennifer, Stephens, Sarah H., Westreich, Samuel T., Prasanna, Anish G., Johanson, Elaine, Boja, Emily, Maier, Ezekiel J., Serang, Omar, Jáspez, David, Lorenzo-Salazar, José M., Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A., Flores, Carlos, Kyriakidis, Konstantinos, Malousi, Andigoni, Shafin, Kishwar, Pesout, Trevor, Jain, Miten, Paten, Benedict, Chang, Pi-Chuan, Kolesnikov, Alexey, Nattestad, Maria, Baid, Gunjan, Goel, Sidharth, Yang, Howard, Carroll, Andrew, Eveleigh, Robert, Bourgey, Mathieu, Bourque, Guillaume, Li, Gen, Ma, ChouXian, Tang, LinQi, Du, YuanPing, Zhang, ShaoWei, Morata, Jordi, Tonda, Raúl, Parra, Genís, Trotta, Jean-Rémi, Brueffer, Christian, Demirkaya-Budak, Sinem, Kabakci-Zorlu, Duygu, Turgut, Deniz, Kalay, Özem, Budak, Gungor, Narcı, Kübra, Arslan, Elif, Brown, Richard, Johnson, Ivan J., Dolgoborodov, Alexey, Semenyuk, Vladimir, Jain, Amit, Tetikol, H. Serhat, Jain, Varun, Ruehle, Mike, Lajoie, Bryan, Roddey, Cooper, Catreux, Severine, Mehio, Rami, Ahsan, Mian Umair, Liu, Qian, Wang, Kai, Ebrahim Sahraeian, Sayed Mohammad, Fang, Li Tai, Mohiyuddin, Marghoob, Hung, Calvin, Jain, Chirag, Feng, Hanying, Li, Zhipan, Chen, Luoqi, Sedlazeck, Fritz J., and Zook, Justin M.

Published
2022
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20. Benchmarking challenging small variants with linked and long reads

Author

Wagner, Justin, Olson, Nathan D., Harris, Lindsay, Khan, Ziad, Farek, Jesse, Mahmoud, Medhat, Stankovic, Ana, Kovacevic, Vladimir, Yoo, Byunggil, Miller, Neil, Rosenfeld, Jeffrey A., Ni, Bohan, Zarate, Samantha, Kirsche, Melanie, Aganezov, Sergey, Schatz, Michael C., Narzisi, Giuseppe, Byrska-Bishop, Marta, Clarke, Wayne, Evani, Uday S., Markello, Charles, Shafin, Kishwar, Zhou, Xin, Sidow, Arend, Bansal, Vikas, Ebert, Peter, Marschall, Tobias, Lansdorp, Peter, Hanlon, Vincent, Mattsson, Carl-Adam, Barrio, Alvaro Martinez, Fiddes, Ian T., Xiao, Chunlin, Fungtammasan, Arkarachai, Chin, Chen-Shan, Wenger, Aaron M., Rowell, William J., Sedlazeck, Fritz J., Carroll, Andrew, Salit, Marc, and Zook, Justin M.

Published
2022
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21. Curated variation benchmarks for challenging medically relevant autosomal genes

Author

Wagner, Justin, Olson, Nathan D., Harris, Lindsay, McDaniel, Jennifer, Cheng, Haoyu, Fungtammasan, Arkarachai, Hwang, Yih-Chii, Gupta, Richa, Wenger, Aaron M., Rowell, William J., Khan, Ziad M., Farek, Jesse, Zhu, Yiming, Pisupati, Aishwarya, Mahmoud, Medhat, Xiao, Chunlin, Yoo, Byunggil, Sahraeian, Sayed Mohammad Ebrahim, Miller, Danny E., Jáspez, David, Lorenzo-Salazar, José M., Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A., Flores, Carlos, Narzisi, Giuseppe, Evani, Uday Shanker, Clarke, Wayne E., Lee, Joyce, Mason, Christopher E., Lincoln, Stephen E., Miga, Karen H., Ebbert, Mark T. W., Shumate, Alaina, Li, Heng, Chin, Chen-Shan, Zook, Justin M., and Sedlazeck, Fritz J.

Published
2022
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22. Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

Author

Pan, Bohu, Ren, Luyao, Onuchic, Vitor, Guan, Meijian, Kusko, Rebecca, Bruinsma, Steve, Trigg, Len, Scherer, Andreas, Ning, Baitang, Zhang, Chaoyang, Glidewell-Kenney, Christine, Xiao, Chunlin, Donaldson, Eric, Sedlazeck, Fritz J., Schroth, Gary, Yavas, Gokhan, Grunenwald, Haiying, Chen, Haodong, Meinholz, Heather, Meehan, Joe, Wang, Jing, Yang, Jingcheng, Foox, Jonathan, Shang, Jun, Miclaus, Kelci, Dong, Lianhua, Shi, Leming, Mohiyuddin, Marghoob, Pirooznia, Mehdi, Gong, Ping, Golshani, Rooz, Wolfinger, Russ, Lababidi, Samir, Sahraeian, Sayed Mohammad Ebrahim, Sherry, Steve, Han, Tao, Chen, Tao, Shi, Tieliu, Hou, Wanwan, Ge, Weigong, Zou, Wen, Guo, Wenjing, Bao, Wenjun, Xiao, Wenzhong, Fan, Xiaohui, Gondo, Yoichi, Yu, Ying, Zhao, Yongmei, Su, Zhenqiang, Liu, Zhichao, Tong, Weida, Xiao, Wenming, Zook, Justin M., Zheng, Yuanting, and Hong, Huixiao

Published
2022
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23. One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation

Author

Lincoln, Stephen E., Hambuch, Tina, Zook, Justin M., Bristow, Sara L., Hatchell, Kathryn, Truty, Rebecca, Kennemer, Michael, Shirts, Brian H., Fellowes, Andrew, Chowdhury, Shimul, Klee, Eric W., Mahamdallie, Shazia, Cleveland, Megan H., Vallone, Peter M., Ding, Yan, Seal, Sheila, DeSilva, Wasanthi, Tomson, Farol L., Huang, Catherine, Garlick, Russell K., Rahman, Nazneen, Salit, Marc, Kingsmore, Stephen F., Ferber, Matthew J., Aradhya, Swaroop, and Nussbaum, Robert L.

Published
2021
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24. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Author

Foox, Jonathan, Tighe, Scott W., Nicolet, Charles M., Zook, Justin M., Byrska-Bishop, Marta, Clarke, Wayne E., Khayat, Michael M., Mahmoud, Medhat, Laaguiby, Phoebe K., Herbert, Zachary T., Warner, Derek, Grills, George S., Jen, Jin, Levy, Shawn, Xiang, Jenny, Alonso, Alicia, Zhao, Xia, Zhang, Wenwei, Teng, Fei, Zhao, Yonggang, Lu, Haorong, Schroth, Gary P., Narzisi, Giuseppe, Farmerie, William, Sedlazeck, Fritz J., Baldwin, Don A., and Mason, Christopher E.

Published
2021
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25. Analysis and benchmarking of small and large genomic variants across tandem repeats

Author

English, Adam C., primary, Dolzhenko, Egor, additional, Ziaei Jam, Helyaneh, additional, McKenzie, Sean K., additional, Olson, Nathan D., additional, De Coster, Wouter, additional, Park, Jonghun, additional, Gu, Bida, additional, Wagner, Justin, additional, Eberle, Michael A., additional, Gymrek, Melissa, additional, Chaisson, Mark J. P., additional, Zook, Justin M., additional, and Sedlazeck, Fritz J., additional

Published
2024
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26. Chromosome-scale, haplotype-resolved assembly of human genomes

Author

Garg, Shilpa, Fungtammasan, Arkarachai, Carroll, Andrew, Chou, Mike, Schmitt, Anthony, Zhou, Xiang, Mac, Stephen, Peluso, Paul, Hatas, Emily, Ghurye, Jay, Maguire, Jared, Mahmoud, Medhat, Cheng, Haoyu, Heller, David, Zook, Justin M., Moemke, Tobias, Marschall, Tobias, Sedlazeck, Fritz J., Aach, John, Chin, Chen-Shan, Church, George M., and Li, Heng

Published
2021
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27. A research roadmap for next-generation sequencing informatics

Author

Altman, Russ B, Prabhu, Snehit, Sidow, Arend, Zook, Justin M, Goldfeder, Rachel, Litwack, David, Ashley, Euan, Asimenos, George, Bustamante, Carlos D, Donigan, Katherine, Giacomini, Kathleen M, Johansen, Elaine, Khuri, Natalia, Lee, Eunice, Liang, Xueying Sharon, Salit, Marc, Serang, Omar, Tezak, Zivana, Wall, Dennis P, Mansfield, Elizabeth, and Kass-Hout, Taha

Subjects
High-Throughput Nucleotide Sequencing, Informatics, Polymorphism, Single Nucleotide, Precision Medicine, Biological Sciences, Medical and Health Sciences
Abstract

Next-generation sequencing technologies are fueling a wave of new diagnostic tests. Progress on a key set of nine research challenge areas will help generate the knowledge required to advance effectively these diagnostics to the clinic.

Published
2016

28. Integrating sequencing datasets to form highly confident SNP and indel genotype calls for a whole human genome

Author

Zook, Justin M., Chapman, Brad, Wang, Jason, Mittelman, David, Hofmann, Oliver, Hide, Winston, and Salit, Marc

Subjects
Quantitative Biology - Genomics
Abstract

Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made clear the need for a highly accurate set of genotypes across a whole genome that could be used as a benchmark. We present methods to make highly confident SNP, indel, and homozygous reference genotype calls for NA12878, the pilot genome for the Genome in a Bottle Consortium. We minimize bias towards any method by integrating and arbitrating between 14 datasets from 5 sequencing technologies, 7 mappers, and 3 variant callers. Regions for which no confident genotype call could be made are identified as uncertain, and classified into different reasons for uncertainty. Our highly confident genotype calls are publicly available on the Genome Comparison and Analytic Testing (GCAT) website to enable real-time benchmarking of any method.

Published
2013
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33. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Author

Wenger, Aaron M., Peluso, Paul, Rowell, William J., Chang, Pi-Chuan, Hall, Richard J., Concepcion, Gregory T., Ebler, Jana, Fungtammasan, Arkarachai, Kolesnikov, Alexey, Olson, Nathan D., Töpfer, Armin, Alonge, Michael, Mahmoud, Medhat, Qian, Yufeng, Chin, Chen-Shan, Phillippy, Adam M., Schatz, Michael C., Myers, Gene, DePristo, Mark A., Ruan, Jue, Marschall, Tobias, Sedlazeck, Fritz J., Zook, Justin M., Li, Heng, Koren, Sergey, Carroll, Andrew, Rank, David R., and Hunkapiller, Michael W.

Published
2019
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35. Benchmarking of small and large variants across tandem repeats

Author

English, Adam, primary, Dolzhenko, Egor, additional, Jam, Helyaneh Ziaei, additional, Mckenzie, Sean, additional, Olson, Nathan D., additional, De Coster, Wouter, additional, Park, Jonghun, additional, Gu, Bida, additional, Wagner, Justin, additional, Eberle, Michael A, additional, Gymrek, Melissa, additional, Chaisson, Mark J.P., additional, Zook, Justin M., additional, and Sedlazeck, Fritz J, additional

Published
2023
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36. Small variant benchmark from a complete assembly of X and Y chromosomes

Author

Wagner, Justin, primary, Olson, Nathan D., additional, McDaniel, Jennifer, additional, Harris, Lindsay, additional, Pinto, Brendan J., additional, Jáspez, David, additional, Muñoz-Barrera, Adrián, additional, Rubio-Rodríguez, Luis A., additional, Lorenzo-Salazar, José M., additional, Flores, Carlos, additional, Ebrahim Sahraeian, Sayed Mohammad, additional, Narzisi, Giuseppe, additional, Byrska-Bishop, Marta, additional, Evani, Uday S, additional, Xiao, Chunlin, additional, Lake, Juniper A., additional, Fontana, Peter, additional, Greenberg, Craig, additional, Freed, Donald, additional, Mootor, Mohammed Faizal Eeman, additional, Boutros, Paul C., additional, Murray, Lisa, additional, Shafin, Kishwar, additional, Carroll, Andrew, additional, Sedlazeck, Fritz J, additional, Wilson, Melissa, additional, and Zook, Justin M., additional

Published
2023
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37. The GIAB genomic stratifications resource for human reference genomes

Author

Dwarshuis, Nathan, primary, Kalra, Divya, additional, McDaniel, Jennifer, additional, Sanio, Philippe, additional, Jerez, Pilar Alvarez, additional, Jadhav, Bharati, additional, Huang, Wenyu (Eddy), additional, Mondal, Rajarshi, additional, Busby, Ben, additional, Olson, Nathan D., additional, Sedlazeck, Fritz J, additional, Wagner, Justin, additional, Majidian, Sina, additional, and Zook, Justin M., additional

Published
2023
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38. Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings

Author

Lubin, Ira M., Aziz, Nazneen, Babb, Lawrence J., Ballinger, Dennis, Bisht, Himani, Church, Deanna M., Cordes, Shaun, Eilbeck, Karen, Hyland, Fiona, Kalman, Lisa, Landrum, Melissa, Lockhart, Edward R., Maglott, Donna, Marth, Gabor, Pfeifer, John D., Rehm, Heidi L., Roy, Somak, Tezak, Zivana, Truty, Rebecca, Ullman-Cullere, Mollie, Voelkerding, Karl V., Worthey, Elizabeth A., Zaranek, Alexander W., and Zook, Justin M.

Published
2017
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39. A diploid assembly-based benchmark for variants in the major histocompatibility complex

Author

Chin, Chen-Shan, Wagner, Justin, Zeng, Qiandong, Garrison, Erik, Garg, Shilpa, Fungtammasan, Arkarachai, Rautiainen, Mikko, Aganezov, Sergey, Kirsche, Melanie, Zarate, Samantha, Schatz, Michael C., Xiao, Chunlin, Rowell, William J., Markello, Charles, Farek, Jesse, Sedlazeck, Fritz J., Bansal, Vikas, Yoo, Byunggil, Miller, Neil, Zhou, Xin, Carroll, Andrew, Barrio, Alvaro Martinez, Salit, Marc, Marschall, Tobias, Dilthey, Alexander T., and Zook, Justin M.

Published
2020
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41. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author

Lee, HoJoon, primary, Greer, Stephanie U., additional, Pavlichin, Dmitri S., additional, Zhou, Bo, additional, Urban, Alexander E., additional, Weissman, Tsachy, additional, Ji, Hanlee P., additional, Liao, Wen-Wei, additional, Asri, Mobin, additional, Ebler, Jana, additional, Doerr, Daniel, additional, Haukness, Marina, additional, Hickey, Glenn, additional, Lu, Shuangjia, additional, Lucas, Julian K., additional, Monlong, Jean, additional, Abel, Haley J., additional, Buonaiuto, Silvia, additional, Chang, Xian H., additional, Cheng, Haoyu, additional, Chu, Justin, additional, Colonna, Vincenza, additional, Eizenga, Jordan M., additional, Feng, Xiaowen, additional, Fischer, Christian, additional, Fulton, Robert S., additional, Garg, Shilpa, additional, Groza, Cristian, additional, Guarracino, Andrea, additional, Harvey, William T., additional, Heumos, Simon, additional, Howe, Kerstin, additional, Jain, Miten, additional, Lu, Tsung-Yu, additional, Markello, Charles, additional, Martin, Fergal J., additional, Mitchell, Matthew W., additional, Munson, Katherine M., additional, Mwaniki, Moses Njagi, additional, Novak, Adam M., additional, Olsen, Hugh E., additional, Pesout, Trevor, additional, Porubsky, David, additional, Prins, Pjotr, additional, Sibbesen, Jonas A., additional, Tomlinson, Chad, additional, Villani, Flavia, additional, Vollger, Mitchell R., additional, Antonacci-Fulton, Lucinda L., additional, Baid, Gunjan, additional, Baker, Carl A., additional, Belyaeva, Anastasiya, additional, Billis, Konstantinos, additional, Carroll, Andrew, additional, Chang, Pi-Chuan, additional, Cody, Sarah, additional, Cook, Daniel E., additional, Cornejo, Omar E., additional, Diekhans, Mark, additional, Ebert, Peter, additional, Fairley, Susan, additional, Fedrigo, Olivier, additional, Felsenfeld, Adam L., additional, Formenti, Giulio, additional, Frankish, Adam, additional, Gao, Yan, additional, Giron, Carlos Garcia, additional, Green, Richard E., additional, Haggerty, Leanne, additional, Hoekzema, Kendra, additional, Hourlier, Thibaut, additional, Kolesnikov, Alexey, additional, Korbel, Jan O., additional, Kordosky, Jennifer, additional, Lee, HoJoon, additional, Lewis, Alexandra P., additional, Magalhães, Hugo, additional, Marco-Sola, Santiago, additional, Marijon, Pierre, additional, McDaniel, Jennifer, additional, Mountcastle, Jacquelyn, additional, Nattestad, Maria, additional, Olson, Nathan D., additional, Puiu, Daniela, additional, Regier, Allison A., additional, Rhie, Arang, additional, Sacco, Samuel, additional, Sanders, Ashley D., additional, Schneider, Valerie A., additional, Schultz, Baergen I., additional, Shafin, Kishwar, additional, Sirén, Jouni, additional, Smith, Michael W., additional, Sofia, Heidi J., additional, Abou Tayoun, Ahmad N., additional, Thibaud-Nissen, Françoise, additional, Tricomi, Francesca Floriana, additional, Wagner, Justin, additional, Wood, Jonathan M.D., additional, Zimin, Aleksey V., additional, Popejoy, Alice B., additional, Bourque, Guillaume, additional, Chaisson, Mark J.P., additional, Flicek, Paul, additional, Phillippy, Adam M., additional, Zook, Justin M., additional, Eichler, Evan E., additional, Haussler, David, additional, Jarvis, Erich D., additional, Miga, Karen H., additional, Wang, Ting, additional, Garrison, Erik, additional, Marschall, Tobias, additional, Hall, Ira, additional, Li, Heng, additional, and Paten, Benedict, additional

Published
2023
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43. Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Author

Foox, Jonathan, Tighe, Scott W., Nicolet, Charles M., Zook, Justin M., Byrska-Bishop, Marta, Clarke, Wayne E., Khayat, Michael M., Mahmoud, Medhat, Laaguiby, Phoebe K., Herbert, Zachary T., Warner, Derek, Grills, George S., Jen, Jin, Levy, Shawn, Xiang, Jenny, Alonso, Alicia, Zhao, Xia, Zhang, Wenwei, Teng, Fei, Zhao, Yonggang, Lu, Haorong, Schroth, Gary P., Narzisi, Giuseppe, Farmerie, William, Sedlazeck, Fritz J., Baldwin, Don A., and Mason, Christopher E.

Published
2021
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45. A draft human pangenome reference

Author

Liao, Wen Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi Chuan, Cody, Sarah, Cook, Daniel E., Cook-Deegan, Robert M., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kenny, Eimear E., Koenig, Barbara A., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, Ho Joon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M.D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Jarvis, Erich D., Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, Paten, Benedict, Liao, Wen Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi Chuan, Cody, Sarah, Cook, Daniel E., Cook-Deegan, Robert M., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kenny, Eimear E., Koenig, Barbara A., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, Ho Joon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M.D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Jarvis, Erich D., Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, and Paten, Benedict

Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals 1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Published
2023

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