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Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers Daniels, Camille A.; Abdulkadir, Adetola A.; Cleveland, Megan H.; McDaniel, Jennifer H.; Jaspez, David; Rubio-Rodrnguez, Luis Alberto; Munoz-Barrera, Adrian; Lorenzo-Salazar, Jose Miguel; Flores, Carlos; Yoo, Byunggil; Sahraeian, Sayed Mohammad Ebrahim; Wang, Yina; Rossi, Massimiliano; Visvanath, Arun; Murray, Lisa; Chen, Wei-Ting; Catreux, Severine; Han, James; Mehio, Rami; Parnaby, Gavin; Carroll, Andrew; Chang, Pi-Chuan; Shafin, Kishwar; Cook, Daniel; Kolesnikov, Alexey; Brambrink, Lucas; Mootor, Mohammed Faizal Eeman; Patel, Yash; Yamaguchi, Takafumi N.; Boutros, Paul C.; Sienkiewicz, Karolina; Foox, Jonathan; Mason, Christopher E.; Lajoie, Bryan R.; Ruiz-Perez, Carlos A.; Kruglyak, Semyon; Zook, Justin M.; Olson, Nathan D. Share Save
Small variant benchmark from a complete assembly of X and Y chromosomes Wagner, Justin; Olson, Nathan D.; Mcdaniel, Jennifer; Harris, Lindsay; Pinto, Brendan J.; Rubio-Rodriguez, Luis A.; Lorenzo-Salazar, Jose M.; Flores, Carlos; Sahraeian, Sayed Mohammad Ebrahim; Narzisi, Giuseppe; Byrska-Bishop, Marta; Evani, Uday S.; Xiao, Chunlin; Lake, Juniper A.; Fontana, Peter; Greenberg, Craig; Freed, Donald; Mootor, Mohammed Faizal Eeman; Boutros, Paul C.; Murray, Lisa; Shafin, Kishwar; Carroll, Andrew; Sedlazeck, Fritz J.; Wilson, Melissa; Zook, Justin M. Share Save
The GIAB genomic stratifications resource for human reference genomes Dwarshuis, Nathan; Kalra, Divya; McDaniel, Jennifer; Sanio, Philippe; Jerez, Pilar Alvarez; Jadhav, Bharati; Huang, Wenyu (Eddy); Mondal, Rajarshi; Busby, Ben; Olson, Nathan D.; Sedlazeck, Fritz J.; Wagner, Justin; Majidian, Sina; Zook, Justin M. Share Save
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High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation Gustafson, Jonas A.; Gibson, Sophia B.; Damaraju, Nikhita; Zalusky, Miranda P. G.; Hoekzema, Kendra; Twesigomwe, David; Yang, Lei; Snead, Anthony A.; Richmond, Phillip A.; De Coster, Wouter; Olson, Nathan D.; Guarracino, Andrea; Li, Qiuhui; Miller, Angela L.; Goffena, Joy; Anderson, Zachary B.; Storz, Sophie H. R.; Ward, Sydney A.; Sinha, Maisha; Gonzaga-Jauregui, Claudia; Clarke, Wayne E.; Basile, Anna O.; Corvelo, Andre; Reeves, Catherine; Helland, Adrienne; Musunuri, Rajeeva Lochan; Revsine, Mahler; Patterson, Karynne E.; Paschal, Cate R.; Zakarian, Christina; Goodwin, Sara; Jensen, Tanner D.; Robb, Esther; McCombie, William Richard; Sedlazeck, Fritz J.; Zook, Justin M.; Montgomery, Stephen B.; Garrison, Erik; Kolmogorov, Mikhail; Schatz, Michael C.; McLaughlin Jr, Richard N.; Dashnow, Harriet; Zody, Michael C.; Loose, Matt; Jain, Miten; Eichler, Evan E.; Miller, Danny E. Share Save
Analysis and benchmarking of small and large genomic variants across tandem repeats English, Adam C.; Dolzhenko, Egor; Jam, Helyaneh Ziaei; Mckenzie, Sean K.; Olson, Nathan D.; De Coster, Wouter; Park, Jonghun; Gu, Bida; Wagner, Justin; Eberle, Michael A.; Gymrek, Melissa; Chaisson, Mark J. P.; Zook, Justin M.; Sedlazeck, Fritz J. Share Save
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Pangenome graph construction from genome alignments with Minigraph-Cactus Hickey, Glenn; Monlong, Jean; Ebler, Jana; Novak, Adam M.; Eizenga, Jordan M.; Gao, Yan; Marschall, Tobias; Li, Heng; Paten, Benedict; Abel, Haley J.; Antonacci-Fulton, Lucinda L.; Asri, Mobin; Baid, Gunjan; Baker, Carl A.; Belyaeva, Anastasiya; Billis, Konstantinos; Bourque, Guillaume; Buonaiuto, Silvia; Carroll, Andrew; Chaisson, Mark J. P.; Chang, Pi-Chuan; Chang, Xian H.; Cheng, Haoyu; Chu, Justin; Cody, Sarah; Colonna, Vincenza; Cook, Daniel E.; Cook-Deegan, Robert M.; Cornejo, Omar E.; Diekhans, Mark; Doerr, Daniel; Ebert, Peter; Ebler, Jana; Eichler, Evan E.; Eizenga, Jordan M.; Fairley, Susan; Fedrigo, Olivier; Felsenfeld, Adam L.; Feng, Xiaowen; Fischer, Christian; Flicek, Paul; Formenti, Giulio; Frankish, Adam; Fulton, Robert S.; Gao, Yan; Garg, Shilpa; Garrison, Erik; Garrison, Nanibaa' A.; Giron, Carlos Garcia; Green, Richard E.; Groza, Cristian; Guarracino, Andrea; Haggerty, Leanne; Hall, Ira M.; Harvey, William T.; Haukness, Marina; Haussler, David; Heumos, Simon; Hickey, Glenn; Hoekzema, Kendra; Hourlier, Thibaut; Howe, Kerstin; Jain, Miten; Jarvis, Erich D.; Ji, Hanlee P.; Kenny, Eimear E.; Koenig, Barbara A.; Kolesnikov, Alexey; Korbel, Jan O.; Kordosky, Jennifer; Koren, Sergey; Lee, HoJoon; Lewis, Alexandra P.; Liao, Wen-Wei; Lu, Shuangjia; Lu, Tsung-Yu; Lucas, Julian K.; Hugo, Magalhaes; Santiago, Marco-Sola; Marijon, Pierre; Markello, Charles; Marschall, Tobias; Martin, Fergal J.; McCartney, Ann; McDaniel, Jennifer; Miga, Karen H.; Mitchell, Matthew W.; Monlong, Jean; Mountcastle, Jacquelyn; Munson, Katherine M.; Mwaniki, Moses Njagi; Nattestad, Maria; Novak, Adam M.; Nurk, Sergey; Olsen, Hugh E.; Olson, Nathan D.; Pesout, Trevor; Phillippy, Adam M.; Popejoy, Alice B.; Porubsky, David; Prins, Pjotr; Puiu, Daniela; Rautiainen, Mikko; Regier, Allison A.; Rhie, Arang; Sacco, Samuel; Sanders, Ashley D.; Schneider, Valerie A.; Schultz, Baergen, I; Shafin, Kishwar; Sibbesen, Jonas A.; Siren, Jouni; Smith, Michael W.; Sofia, Heidi J.; Abou Tayoun, Ahmad N.; Thibaud-Nissen, Francoise; Tomlinson, Chad; Tricomi, Francesca Floriana; Villani, Flavia; Vollger, Mitchell R.; Wagner, Justin; Walenz, Brian; Wang, Ting; Wood, Jonathan M. D.; Zimin, Aleksey, V; Zook, Justin M. Share Save
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PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions 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; Jaspez, David; Lorenzo-Salazar, Jose M.; Munoz-Barrera, Adrian; Rubio-Rodriguez, 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, Raul; Parra, Genis; Trotta, Jean-Remi; Brueffer, Christian; Demirkaya-Budak, Sinem; Kabakci-Zorlu, Duygu; Turgut, Deniz; Kalay, Ozem; Narci, Kubra; 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; Sahraeian, Sayed Mohammad Ebrahim; Fang, Li Tai; Mohiyuddin, Marghoob; Hung, Calvin; Jain, Chirag; Feng, Hanying; Li, Zhipan; Chen, Luoqi; Sedlazeck, Fritz J.; Zook, Justin M. Share Save
Benchmarking challenging small variants with linked and long reads 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. Share Save
Curated variation benchmarks for challenging medically relevant autosomal genes 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.; Jaspez, David; Lorenzo-Salazar, Jose M.; Munoz-Barrera, Adrian; Rubio-Rodriguez, 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.; Sedlazeck, Fritz J. Share Save
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Zero-Valent Iron Sand Filtration Can Reduce Human and Plant Pathogenic Bacteria While Increasing Plant Growth Promoting Bacteria in Reclaimed Water Kulkarni, Prachi; Olson, Nathan D.; Bui, Anthony Q.; Bradshaw, Rhodel N.; Del Collo, Laura P.; Hittle, Lauren E.; Handy, Eric T.; Paulson, Joseph N.; Ghurye, Jay; Nasko, Daniel J.; East, Cheryl; Van Kessel, Jo Ann; Kniel, Kalmia E.; Chiu, Pei C.; Mongodin, Emmanuel F.; Pop, Mihai; Sharma, Manan; Sapkota, Amy R. Share Save
A robust benchmark for detection of germline large deletions and insertions (Jun, 10.1038/s41587-020-0538-8, 2020) 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 J. P.; Spies, Noah; Sedlazeck, Fritz J.; Salit, Marc Share Save
A robust benchmark for detection of germline large deletions and insertions 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 J. P.; Spies, Noah; Sedlazeck, Fritz J.; Salit, Marc Share Save
Assembly and annotation of an Ashkenazi human reference genome Shumate, Alaina; Zimin, Aleksey, V; Sherman, Rachel M.; Puiu, Daniela; Wagner, Justin M.; Olson, Nathan D.; Pertea, Mihaela; Salit, Marc L.; Zook, Justin M.; Salzberg, Steven L. Share Save
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