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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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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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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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 graph indexes von Sirén, Jouni, Garrison, Erik, Novak, Adam M, 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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Haplotype-aware diplotyping from noisy long reads von Ebler, Jana, Haukness, Marina, Pesout, Trevor, Marschall, Tobias, 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., Siren, 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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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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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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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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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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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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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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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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