TT-Mars: structural variants assessment based on haplotype-resolved assemblies von Yang, Jianzhi, Chaisson, Mark J P

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Genetic variation and the de novo assembly of human genomes von Chaisson, Mark J. P., Wilson, Richard K., Eichler, Evan E.

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Resolving the complexity of the human genome using single-molecule sequencing von Chaisson, Mark J. P., Huddleston, John, Dennis, Megan Y., Sudmant, Peter H., Malig, Maika, Hormozdiari, Fereydoun, Antonacci, Francesca, Surti, Urvashi, Sandstrom, Richard, Boitano, Matthew, Landolin, Jane M., Stamatoyannopoulos, John A., Hunkapiller, Michael W., Korlach, Jonas, Eichler, Evan E.

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Discovery and genotyping of structural variation from long-read haploid genome sequence data von Huddleston, John, Chaisson, Mark J P, Steinberg, Karyn Meltz, Warren, Wes, Hoekzema, Kendra, Gordon, David, Graves-Lindsay, Tina A, Munson, Katherine M, Kronenberg, Zev N, Vives, Laura, Peluso, Paul, Boitano, Matthew, Chin, Chen-Shin, Korlach, Jonas, Wilson, Richard K, Eichler, Evan E

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Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants von Lin, Jiadong, Yang, Xiaofei, Kosters, Walter, Xu, Tun, Jia, Yanyan, Wang, Songbo, Zhu, Qihui, Ryan, Mallory, Guo, Li, Zhang, Chengsheng, Gerstein, Mark B., Sanders, Ashley D., Zody, Micheal C., Talkowski, Michael E., Mills, Ryan E., Korbel, Jan O., Marschall, Tobias, Ebert, Peter, Audano, Peter A., Rodriguez-Martin, Bernardo, Porubsky, David, Jan Bonder, Marc, Sulovari, Arvis, Ebler, Jana, Zhou, Weichen, Serra Mari, Rebecca, Yilmaz, Feyza, Zhao, Xuefang, Hsieh, PingHsun, Lee, Joyce, Kumar, Sushant, Rausch, Tobias, Chen, Yu, Chong, Zechen, Munson, Katherine M., Chaisson, Mark J.P., Chen, Junjie, Shi, Xinghua, Wenger, Aaron M., Harvey, William T., Hansenfeld, Patrick, Regier, Allison, Hall, Ira M., Flicek, Paul, Hastie, Alex R., Fairely, Susan, Lee, Charles, Devine, Scott E., Eichler, Evan E., Ye, Kai

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lra: A long read aligner for sequences and contigs von Ren, Jingwen, Chaisson, Mark J P

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vamos: variable-number tandem repeats annotation using efficient motif sets von Ren, Jingwen, Gu, Bida, Chaisson, Mark J P

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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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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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An integrated map of structural variation in 2,504 human genomes von Sudmant, Peter H., Rausch, Tobias, Gardner, Eugene J., Handsaker, Robert E., Abyzov, Alexej, Huddleston, John, Zhang, Yan, Ye, Kai, Jun, Goo, Hsi-Yang Fritz, Markus, Konkel, Miriam K., Malhotra, Ankit, Stütz, Adrian M., Shi, Xinghua, Paolo Casale, Francesco, Chen, Jieming, Hormozdiari, Fereydoun, Dayama, Gargi, Chen, Ken, Malig, Maika, Chaisson, Mark J. P., Walter, Klaudia, Meiers, Sascha, Kashin, Seva, Garrison, Erik, Auton, Adam, Lam, Hugo Y. K., Jasmine Mu, Xinmeng, Alkan, Can, Antaki, Danny, Bae, Taejeong, Cerveira, Eliza, Chines, Peter, Chong, Zechen, Clarke, Laura, Dal, Elif, Ding, Li, Emery, Sarah, Fan, Xian, Gujral, Madhusudan, Kahveci, Fatma, Kidd, Jeffrey M., Kong, Yu, Lameijer, Eric-Wubbo, McCarthy, Shane, Flicek, Paul, Gibbs, Richard A., Marth, Gabor, Mason, Christopher E., Menelaou, Androniki, Muzny, Donna M., Nelson, Bradley J., Noor, Amina, Parrish, Nicholas F., Pendleton, Matthew, Quitadamo, Andrew, Raeder, Benjamin, Schadt, Eric E., Romanovitch, Mallory, Schlattl, Andreas, Sebra, Robert, Shabalin, Andrey A., Untergasser, Andreas, Walker, Jerilyn A., Wang, Min, Yu, Fuli, Zhang, Chengsheng, Zhang, Jing, Zheng-Bradley, Xiangqun, Zhou, Wanding, Zichner, Thomas, Sebat, Jonathan, Batzer, Mark A., McCarroll, Steven A., Mills, Ryan E., Gerstein, Mark B., Bashir, Ali, Stegle, Oliver, Devine, Scott E., Lee, Charles, Eichler, Evan E., Korbel, Jan O.

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HQAlign: aligning nanopore reads for SV detection using current-level modeling von Joshi, Dhaivat, Diggavi, Suhas, Chaisson, Mark J P, Kannan, Sreeram

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Long-read sequence assembly of the gorilla genome von Gordon, David, Huddleston, John, Chaisson, Mark J. P., Hill, Christopher M., Kronenberg, Zev N., Munson, Katherine M., Malig, Maika, Raja, Archana, Fiddes, Ian, Hillier, LaDeana W., Dunn, Christopher, Baker, Carl, Armstrong, Joel, Diekhans, Mark, Paten, Benedict, Shendure, Jay, Wilson, Richard K., Haussler, David, Chin, Chen-Shan, Eichler, Evan E.

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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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Long-read sequence and assembly of segmental duplications von Vollger, Mitchell R., Dishuck, Philip C., Sorensen, Melanie, Welch, AnneMarie E., Dang, Vy, Dougherty, Max L., Graves-Lindsay, Tina A., Wilson, Richard K., Chaisson, Mark J. P., Eichler, Evan E.

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The motif composition of variable number tandem repeats impacts gene expression von Lu, Tsung-Yu, Smaruj, Paulina N, Fudenberg, Geoffrey, Mancuso, Nicholas, Chaisson, Mark J P

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Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies von Zhao, Xuefang, Collins, Ryan L., Lee, Wan-Ping, Weber, Alexandra M., Jun, Yukyung, Zhu, Qihui, Weisburd, Ben, Huang, Yongqing, Audano, Peter A., Wang, Harold, Walker, Mark, Lowther, Chelsea, Fu, Jack, Gerstein, Mark B., Devine, Scott E., Marschall, Tobias, Korbel, Jan O., Eichler, Evan E., Chaisson, Mark J.P., Lee, Charles, Mills, Ryan E., Brand, Harrison, Talkowski, Michael E.

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Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs von Lu, Tsung-Yu, Chaisson, Mark J. P.

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Analysis and benchmarking of small and large genomic variants across tandem repeats von English, Adam C, Dolzhenko, Egor, Ziaei Jam, Helyaneh, 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

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Human-specific tandem repeat expansion and differential gene expression during primate evolution von Sulovari, Arvis, Li, Ruiyang, Audano, Peter A., Porubsky, David, Vollger, Mitchell R., Logsdon, Glennis A., Warren, Wesley C., Pollen, Alex A., Chaisson, Mark J. P., Eichler, Evan E.

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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy von Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Grüning, Bjorn, Ko, Byung June, Ostrovsky, Alex, Palmada-Flores, Marc, Pickett, Brandon D., Rabbani, Keon, Antunes, Agostinho, Balacco, Jennifer R., Chaisson, Mark J. P., Cheng, Haoyu, Collins, Joanna, Couture, Melanie, Denisova, Alexandra, Fedrigo, Olivier, Gallo, Guido Roberto, Giani, Alice Maria, Gooder, Grenville MacDonald, Horan, Kathleen, Jain, Nivesh, Johnson, Cassidy, Kim, Heebal, Lee, Chul, Marques-Bonet, Tomas, O’Toole, Brian, Rhie, Arang, Secomandi, Simona, Sozzoni, Marcella, Tilley, Tatiana, Uliano-Silva, Marcela, van den Beek, Marius, Williams, Robert W., Waterhouse, Robert M., Phillippy, Adam M., Jarvis, Erich D., Schatz, Michael C., Nekrutenko, Anton, Formenti, Giulio

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