YaHS: yet another Hi-C scaffolding tool von Zhou, Chenxi, McCarthy, Shane A, Durbin, Richard

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BCFtools/csq: haplotype-aware variant consequences von Danecek, Petr, McCarthy, Shane A

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Identifying and removing haplotypic duplication in primary genome assemblies von Guan, Dengfeng, McCarthy, Shane A, Wood, Jonathan, Howe, Kerstin, Wang, Yadong, Durbin, Richard

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Twelve years of SAMtools and BCFtools von Danecek, Petr, Bonfield, James K, Liddle, Jennifer, Marshall, John, Ohan, Valeriu, Pollard, Martin O, Whitwham, Andrew, Keane, Thomas, McCarthy, Shane A, Davies, Robert M, Li, Heng

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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads von Uliano-Silva, Marcela, Ferreira, João Gabriel R N, Krasheninnikova, Ksenia, Formenti, Giulio, Abueg, Linelle, Torrance, James, Myers, Eugene W, Durbin, Richard, Blaxter, Mark, McCarthy, Shane A

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Insights into human genetic variation and population history from 929 diverse genomes von Bergström, Anders, McCarthy, Shane A, Hui, Ruoyun, Almarri, Mohamed A, Ayub, Qasim, Danecek, Petr, Chen, Yuan, Felkel, Sabine, Hallast, Pille, Kamm, Jack, Blanché, Hélène, Deleuze, Jean-François, Cann, Howard, Mallick, Swapan, Reich, David, Sandhu, Manjinder S, Skoglund, Pontus, Scally, Aylwyn, Xue, Yali, Durbin, Richard, Tyler-Smith, Chris

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Rare structural variants in schizophrenia: one disorder, multiple mutations; one mutation, multiple disorders von Sebat, Jonathan, Levy, Deborah L, McCarthy, Shane E

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Reference-based phasing using the Haplotype Reference Consortium panel von Loh, Po-Ru, Danecek, Petr, Palamara, Pier Francesco, Fuchsberger, Christian, A Reshef, Yakir, K Finucane, Hilary, Schoenherr, Sebastian, Forer, Lukas, McCarthy, Shane, Abecasis, Goncalo R, Durbin, Richard, L Price, Alkes

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A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data von Danecek, Petr, McCarthy, Shane A, Durbin, Richard

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Efficient iterative Hi-C scaffolder based on N-best neighbors von Guan, Dengfeng, McCarthy, Shane A, Ning, Zemin, Wang, Guohua, Wang, Yadong, Durbin, Richard

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Common genetic variation drives molecular heterogeneity in human iPSCs von Kilpinen, Helena, Goncalves, Angela, Leha, Andreas, Afzal, Vackar, Alasoo, Kaur, Ashford, Sofie, Bala, Sendu, Bensaddek, Dalila, Casale, Francesco Paolo, Culley, Oliver J., Danecek, Petr, Faulconbridge, Adam, Harrison, Peter W., Kathuria, Annie, McCarthy, Davis, McCarthy, Shane A., Meleckyte, Ruta, Memari, Yasin, Moens, Nathalie, Soares, Filipa, Mann, Alice, Streeter, Ian, Agu, Chukwuma A., Alderton, Alex, Nelson, Rachel, Harper, Sarah, Patel, Minal, White, Alistair, Patel, Sharad R., Clarke, Laura, Halai, Reena, Kirton, Christopher M., Kolb-Kokocinski, Anja, Beales, Philip, Birney, Ewan, Danovi, Davide, Lamond, Angus I., Ouwehand, Willem H., Vallier, Ludovic, Watt, Fiona M., Durbin, Richard, Stegle, Oliver, Gaffney, Daniel J.

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The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies von Copin, Richard, Baum, Alina, Wloga, Elzbieta, Pascal, Kristen E., Giordano, Stephanie, Fulton, Benjamin O., Zhou, Anbo, Negron, Nicole, Lanza, Kathryn, Chan, Newton, Coppola, Angel, Chiu, Joyce, Ni, Min, Wei, Yi, Atwal, Gurinder S., Hernandez, Annabel Romero, Saotome, Kei, Zhou, Yi, Franklin, Matthew C., Hooper, Andrea T., McCarthy, Shane, Hamon, Sara, Hamilton, Jennifer D., Staples, Hilary M., Alfson, Kendra, Carrion, Ricardo, Ali, Shazia, Norton, Thomas, Somersan-Karakaya, Selin, Sivapalasingam, Sumathi, Herman, Gary A., Weinreich, David M., Lipsich, Leah, Stahl, Neil, Murphy, Andrew J., Yancopoulos, George D., Kyratsous, Christos A.

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Crumble: reference free lossy compression of sequence quality values von Bonfield, James K, McCarthy, Shane A, Durbin, Richard

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Genomics of cold adaptations in the Antarctic notothenioid fish radiation von Bista, Iliana, Wood, Jonathan M. D., Desvignes, Thomas, McCarthy, Shane A., Matschiner, Michael, Ning, Zemin, Tracey, Alan, Torrance, James, Sims, Ying, Chow, William, Smith, Michelle, Oliver, Karen, Haggerty, Leanne, Salzburger, Walter, Postlethwait, John H., Howe, Kerstin, Clark, Melody S., William Detrich, H., Christina Cheng, C.-H., Miska, Eric A., Durbin, Richard

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A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.) von Generalovic, Tomas N, McCarthy, Shane A, Warren, Ian A, Wood, Jonathan M D, Torrance, James, Sims, Ying, Quail, Michael, Howe, Kerstin, Pipan, Miha, Durbin, Richard, Jiggins, Chris D

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Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors von Guan, Dengfeng, McCarthy, Shane A, Ning, Zemin, Wang, Guohua, Wang, Yadong, Durbin, Richard

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Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians von Ovchinnikov, Vladimir, Uliano-Silva, Marcela, Wilkinson, Mark, Wood, Jonathan, Smith, Michelle, Oliver, Karen, Sims, Ying, Torrance, James, Suh, Alexander, McCarthy, Shane A, Durbin, Richard, O’Connell, Mary J

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Complete vertebrate mitogenomes reveal widespread repeats and gene duplications von Formenti, Giulio, Rhie, Arang, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O, Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Kwak, Woori, Korlach, Jonas, Fungtammasan, Arkarachai, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S, Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L, Phillippy, Adam M, Jarvis, Erich D

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Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7 von Luo, Yang, de Lange, Katrina M, Jostins, Luke, Moutsianas, Loukas, Randall, Joshua, Kennedy, Nicholas A, Lamb, Christopher A, McCarthy, Shane, Ahmad, Tariq, Edwards, Cathryn, Serra, Eva Goncalves, Hart, Ailsa, Hawkey, Chris, Mansfield, John C, Mowat, Craig, Newman, William G, Nichols, Sam, Pollard, Martin, Satsangi, Jack, Simmons, Alison, Tremelling, Mark, Uhlig, Holm, Wilson, David C, Lee, James C, Prescott, Natalie J, Lees, Charlie W, Mathew, Christopher G, Parkes, Miles, Barrett, Jeffrey C, Anderson, Carl A

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The gene-rich genome of the scallop Pecten maximus von Kenny, Nathan J, McCarthy, Shane A, Dudchenko, Olga, James, Katherine, Betteridge, Emma, Corton, Craig, Dolucan, Jale, Mead, Dan, Oliver, Karen, Omer, Arina D, Pelan, Sarah, Ryan, Yan, Sims, Ying, Skelton, Jason, Smith, Michelle, Torrance, James, Weisz, David, Wipat, Anil, Aiden, Erez L, Howe, Kerstin, Williams, Suzanne T

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