The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community von Jain, Miten, Olsen, Hugh E, Paten, Benedict, Akeson, Mark

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Genome graphs and the evolution of genome inference von Paten, Benedict, Novak, Adam M, Eizenga, Jordan M, Garrison, Erik

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Ragout-a reference-assisted assembly tool for bacterial genomes von Kolmogorov, Mikhail, Raney, Brian, Paten, Benedict, Pham, Son

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Haplotype-aware graph indexes von Sirén, Jouni, Garrison, Erik, Novak, Adam M, Paten, Benedict, Durbin, Richard

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Variation graph toolkit improves read mapping by representing genetic variation in the reference von Garrison, Erik, Sirén, Jouni, Novak, Adam M, Hickey, Glenn, Eizenga, Jordan M, Dawson, Eric T, Jones, William, Garg, Shilpa, Markello, Charles, Lin, Michael F, Paten, Benedict, Durbin, Richard

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Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads von Shafin, Kishwar, Pesout, Trevor, Chang, Pi-Chuan, Nattestad, Maria, Kolesnikov, Alexey, Goel, Sidharth, Baid, Gunjan, Kolmogorov, Mikhail, Eizenga, Jordan M., Miga, Karen H., Carnevali, Paolo, Jain, Miten, Carroll, Andrew, Paten, Benedict

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Genotyping structural variants in pangenome graphs using the vg toolkit von Hickey, Glenn, Heller, David, Monlong, Jean, Sibbesen, Jonas A, Sirén, Jouni, Eizenga, Jordan, Dawson, Eric T, Garrison, Erik, Novak, Adam M, Paten, Benedict

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Progressive Cactus is a multiple-genome aligner for the thousand-genome era von Armstrong, Joel, Hickey, Glenn, Diekhans, Mark, Fiddes, Ian T., Novak, Adam M., Deran, Alden, Fang, Qi, Xie, Duo, Feng, Shaohong, Stiller, Josefin, Genereux, Diane, Johnson, Jeremy, Marinescu, Voichita Dana, Alföldi, Jessica, Harris, Robert S., Lindblad-Toh, Kerstin, Haussler, David, Karlsson, Elinor, Jarvis, Erich D., Zhang, Guojie, Paten, Benedict

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Haplotype-aware diplotyping from noisy long reads von Ebler, Jana, Haukness, Marina, Pesout, Trevor, Marschall, Tobias, Paten, Benedict

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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes von 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, Paten, Benedict

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Linear assembly of a human centromere on the Y chromosome von Jain, Miten, Olsen, Hugh E, Turner, Daniel J, Stoddart, David, Bulazel, Kira V, Paten, Benedict, Haussler, David, Willard, Huntington F, Akeson, Mark, Miga, Karen H

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HAL: a hierarchical format for storing and analyzing multiple genome alignments von Hickey, Glenn, Paten, Benedict, Earl, Dent, Zerbino, Daniel, Haussler, David

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An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons von Jacobs, Frank M. J., Greenberg, David, Nguyen, Ngan, Haeussler, Maximilian, Ewing, Adam D., Katzman, Sol, Paten, Benedict, Salama, Sofie R., Haussler, David

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The Human Pangenome Project: a global resource to map genomic diversity von Wang, Ting, Antonacci-Fulton, Lucinda, Howe, Kerstin, Lawson, Heather A., Lucas, Julian K., Phillippy, Adam M., Popejoy, Alice B., Asri, Mobin, Carson, Caryn, Chaisson, Mark J. P., Chang, Xian, Cook-Deegan, Robert, Felsenfeld, Adam L., Fulton, Robert S., Garrison, Erik P., Garrison, Nanibaa’ A., Graves-Lindsay, Tina A., Ji, Hanlee, Kenny, Eimear E., Koenig, Barbara A., Li, Daofeng, Marschall, Tobias, McMichael, Joshua F., Novak, Adam M., Purushotham, Deepak, Schneider, Valerie A., Schultz, Baergen I., Smith, Michael W., Sofia, Heidi J., Weissman, Tsachy, Flicek, Paul, Li, Heng, Miga, Karen H., Paten, Benedict, Jarvis, Erich D., Hall, Ira M., Eichler, Evan E., Haussler, David

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Pangenome Graphs von Eizenga, Jordan M, Novak, Adam M, Sibbesen, Jonas A, Heumos, Simon, Ghaffaari, Ali, Hickey, Glenn, Chang, Xian, Seaman, Josiah D, Rounthwaite, Robin, Ebler, Jana, Rautiainen, Mikko, Garg, Shilpa, Paten, Benedict, Marschall, Tobias, Sirén, Jouni, Garrison, Erik

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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads von Porubsky, David, Ebert, Peter, Audano, Peter A., Vollger, Mitchell R., Harvey, William T., Marijon, Pierre, Ebler, Jana, Munson, Katherine M., Sorensen, Melanie, Sulovari, Arvis, Haukness, Marina, Ghareghani, Maryam, Lansdorp, Peter M., Paten, Benedict, Devine, Scott E., Sanders, Ashley D., Lee, Charles, Chaisson, Mark J. P., Korbel, Jan O., Eichler, Evan E., Marschall, Tobias

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Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures von Ding, Hongxu, Anastopoulos, Ioannis, Bailey, Andrew D., Stuart, Joshua, Paten, Benedict

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Cactus: Algorithms for genome multiple sequence alignment von Paten, Benedict, Earl, Dent, Nguyen, Ngan, Diekhans, Mark, Zerbino, Daniel, Haussler, David

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Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser von Raney, Brian J, Dreszer, Timothy R, Barber, Galt P, Clawson, Hiram, Fujita, Pauline A, Wang, Ting, Nguyen, Ngan, Paten, Benedict, Zweig, Ann S, Karolchik, Donna, Kent, W James

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High-resolution comparative analysis of great ape genomes von Kronenberg, Zev N, Fiddes, Ian T, Gordon, David, Murali, Shwetha, Cantsilieris, Stuart, Meyerson, Olivia S, Underwood, Jason G, Nelson, Bradley J, Chaisson, Mark J P, Dougherty, Max L, Munson, Katherine M, Hastie, Alex R, Diekhans, Mark, Hormozdiari, Fereydoun, Lorusso, Nicola, Hoekzema, Kendra, Qiu, Ruolan, Clark, Karen, Raja, Archana, Welch, AnneMarie E, Sorensen, Melanie, Baker, Carl, Fulton, Robert S, Armstrong, Joel, Graves-Lindsay, Tina A, Denli, Ahmet M, Hoppe, Emma R, Hsieh, PingHsun, Hill, Christopher M, Pang, Andy Wing Chun, Lee, Joyce, Lam, Ernest T, Dutcher, Susan K, Gage, Fred H, Warren, Wesley C, Shendure, Jay, Haussler, David, Schneider, Valerie A, Cao, Han, Ventura, Mario, Wilson, Richard K, Paten, Benedict, Pollen, Alex, Eichler, Evan E

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