Identifying and removing haplotypic duplication in primary genome assemblies
Guan, Dengfeng, McCarthy, Shane A, Wood, Jonathan, Howe, Kerstin, Wang, Yadong, Durbin, Richard
Published in Bioinformatics (01.05.2020)
Published in Bioinformatics (01.05.2020)
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Journal Article
Twelve years of SAMtools and BCFtools
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
Published in Gigascience (16.02.2021)
Published in Gigascience (16.02.2021)
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Journal Article
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
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
Published in BMC bioinformatics (18.07.2023)
Published in BMC bioinformatics (18.07.2023)
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Journal Article
Efficient iterative Hi-C scaffolder based on N-best neighbors
Guan, Dengfeng, McCarthy, Shane A, Ning, Zemin, Wang, Guohua, Wang, Yadong, Durbin, Richard
Published in BMC bioinformatics (27.11.2021)
Published in BMC bioinformatics (27.11.2021)
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Journal Article
YaHS: yet another Hi-C scaffolding tool
Zhou, Chenxi, McCarthy, Shane A, Durbin, Richard
Published in Bioinformatics (Oxford, England) (01.01.2023)
Published in Bioinformatics (Oxford, England) (01.01.2023)
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Journal Article
Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors
Guan, Dengfeng, McCarthy, Shane A, Ning, Zemin, Wang, Guohua, Wang, Yadong, Durbin, Richard
Published in BMC bioinformatics (31.12.2021)
Published in BMC bioinformatics (31.12.2021)
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Journal Article
The gene-rich genome of the scallop Pecten maximus
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
Published in Gigascience (01.05.2020)
Published in Gigascience (01.05.2020)
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Journal Article
A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)
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
Published in G3 : genes - genomes - genetics (01.05.2021)
Published in G3 : genes - genomes - genetics (01.05.2021)
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Journal Article
The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens
Aunin, Eerik, Böhme, Ulrike, Blake, Damer, Dove, Alexander, Smith, Michelle, Corton, Craig, Oliver, Karen, Betteridge, Emma, Quail, Michael A., McCarthy, Shane A., Wood, Jonathan, Tracey, Alan, Torrance, James, Sims, Ying, Howe, Kerstin, Challis, Richard, Berriman, Matthew, Reid, Adam
Published in Wellcome open research (2021)
Published in Wellcome open research (2021)
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Journal Article
The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769
Howe, Kerstin, Dwinell, Melinda, Shimoyama, Mary, Corton, Craig, Betteridge, Emma, Dove, Alexander, Quail, Michael A., Smith, Michelle, Saba, Laura, Williams, Robert W., Chen, Hao, Kwitek, Anne E., McCarthy, Shane A., Uliano-Silva, Marcela, Chow, William, Tracey, Alan, Torrance, James, Sims, Ying, Challis, Richard, Threlfall, Jonathan, Blaxter, Mark
Published in Wellcome open research (2021)
Published in Wellcome open research (2021)
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Journal Article
The genome sequence of the brown trout, Salmo trutta Linnaeus 1758
Hansen, Tom, Fjelldal, Per Gunnar, Lien, Sigbjørn, Smith, Michelle, Corton, Craig, Oliver, Karen, Skelton, Jason, Betteridge, Emma, Doulcan, Jale, Fedrigo, Olivier, Mountcastle, Jacquelyn, Jarvis, Erich, McCarthy, Shane A., Chow, William, Howe, Kerstin, Torrance, James, Wood, Jonathan, Sims, Ying, Haggerty, Leanne, Challis, Richard, Threlfall, Jonathan, Mead, Daniel, Durbin, Richard, Blaxter, Mark
Published in Wellcome open research (2021)
Published in Wellcome open research (2021)
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Journal Article
Insights into human genetic variation and population history from 929 diverse genomes
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
Published in Science (American Association for the Advancement of Science) (20.03.2020)
Published in Science (American Association for the Advancement of Science) (20.03.2020)
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Journal Article
A chromosomal reference genome sequence for the malaria mosquito, Anopheles moucheti , Evans, 1925
Nsango, Sandrine N, Agbor, Jean-Pierre, Ayala, Diego, Johnson, Harriet F, Heaton, Haynes, Wagah, Martin G, Collins, Joanna C, Krasheninnikova, Ksenia, Pelan, Sarah E, Pointon, Damon-Lee B, Sims, Ying, Torrance, James W, Tracey, Alan, Uliano Da Silva, Marcela, Wood, Jonathan M D, von Wyschetzki, Katharina, McCarthy, Shane A, Neafsey, Daniel E, Makunin, Alex, Lawniczak, Mara
Published in Wellcome open research (2023)
Published in Wellcome open research (2023)
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Journal Article
The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861)
Bista, Iliana, McCarthy, Shane A, Wood, Jonathan, Ning, Zemin, Detrich Iii, H William, Desvignes, Thomas, Postlethwait, John, Chow, William, Howe, Kerstin, Torrance, James, Smith, Michelle, Oliver, Karen, Miska, Eric A, Durbin, Richard
Published in Wellcome open research (2020)
Published in Wellcome open research (2020)
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Journal Article
A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae , Giles, 1902, Ifakara strain
Habtewold, Tibebu, Wagah, Martin, Tambwe, Mgeni Mohamed, Moore, Sarah, Windbichler, Nikolai, Christophides, George, Johnson, Harriet, Heaton, Haynes, Collins, Joanna, Krasheninnikova, Ksenia, Pelan, Sarah E, Pointon, Damon-Lee B, Sims, Ying, Torrance, James W, Tracey, Alan, Uliano Da Silva, Marcela, Wood, Jonathan Md, von Wyschetzki, Katharina, McCarthy, Shane A, Neafsey, Daniel E, Makunin, Alex, Lawniczak, Mara K N, Lawniczak, Mara
Published in Wellcome open research (2023)
Published in Wellcome open research (2023)
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Journal Article
The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758
Mead, Dan, Ogden, Rob, Meredith, Anna, Peniche, Gabriela, Smith, Michelle, Corton, Craig, Oliver, Karen, Skelton, Jason, Betteridge, Emma, Doulcan, Jale, Holmes, Nadine, Wright, Victoria, Loose, Matt, Quail, Michael A., McCarthy, Shane A., Howe, Kerstin, Chow, William, Torrance, James, Collins, Joanna, Challis, Richard, Durbin, Richard, Blaxter, Mark
Published in Wellcome open research (2021)
Published in Wellcome open research (2021)
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Journal Article
The genome sequence of the European water vole, Arvicola amphibius Linnaeus 1758
Carpenter, Angus I, Smith, Michelle, Corton, Craig, Oliver, Karen, Skelton, Jason, Betteridge, Emma, Doulcan, Jale, Quail, Michael A, McCarthy, Shane A, Uliano Da Silva, Marcela, Howe, Kerstin, Torrance, James, Wood, Jonathan, Pelan, Sarah, Sims, Ying, Tricomi, Francesca Floriana, Challis, Richard, Threlfall, Jonathan, Mead, Daniel, Blaxter, Mark
Published in Wellcome open research (2021)
Published in Wellcome open research (2021)
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Journal Article