Local read haplotagging enables accurate long-read small variant calling

por Kolesnikov, Alexey, Cook, Daniel, Nattestad, Maria, McNulty, Brandy, Gorzynski, John, Goenka, Sneha, Ashley, Euan A., Jain, Miten, Miga, Karen H., Paten, Benedict, Chang, Pi-Chuan, Carroll, Andrew, Shafin, Kishwar
Publicado 2023

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

por 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
Publicado 2021

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

por Kolmogorov, Mikhail, Billingsley, Kimberley J., Mastoras, Mira, Meredith, Melissa, Monlong, Jean, Lorig-Roach, Ryan, Asri, Mobin, Jerez, Pilar Alvarez, Malik, Laksh, Dewan, Ramita, Reed, Xylena, Genner, Rylee M., Daida, Kensuke, Behera, Sairam, Shafin, Kishwar, Pesout, Trevor, Prabakaran, Jeshuwin, Carnevali, Paolo, Yang, Jianzhi, Rhie, Arang, Scholz, Sonja W., Traynor, Bryan J., Miga, Karen H., Jain, Miten, Timp, Winston, Phillippy, Adam M., Chaisson, Mark, Sedlazeck, Fritz J., Blauwendraat, Cornelis, Paten, Benedict
Publicado 2023

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

por 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
Publicado 2020

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

por Goenka, Sneha D., Gorzynski, John E., Shafin, Kishwar, Fisk, Dianna G., Pesout, Trevor, Jensen, Tanner D., Monlong, Jean, Chang, Pi-Chuan, Baid, Gunjan, Bernstein, Jonathan A., Christle, Jeffrey W., Dalton, Karen P., Garalde, Daniel R., Grove, Megan E., Guillory, Joseph, Kolesnikov, Alexey, Nattestad, Maria, Ruzhnikov, Maura R. Z., Samadi, Mehrzad, Sethia, Ankit, Spiteri, Elizabeth, Wright, Christopher J., Xiong, Katherine, Zhu, Tong, Jain, Miten, Sedlazeck, Fritz J., Carroll, Andrew, Paten, Benedict, Ashley, Euan A.
Publicado 2022

Benchmarking challenging small variants with linked and long reads

por 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, Zook, Justin M.
Publicado 2022

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

por 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., Zook, Justin M.
Publicado 2022

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

por 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 J. P., 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, Miga, Karen H.
Publicado 2022

The complete sequence of a human genome*

por 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 G.S., 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 F. A., 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 M. D., 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., Phillippy, Adam M.
Publicado 2022

A draft human pangenome reference

por 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, Paten, Benedict
Publicado 2023