BCFtools/csq: haplotype-aware variant consequences

por Danecek, Petr, McCarthy, Shane A
Publicado 2017

A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data

por Danecek, Petr, McCarthy, Shane A., Durbin, Richard
Publicado 2016

YaHS: yet another Hi-C scaffolding tool

por Zhou, Chenxi, McCarthy, Shane A, Durbin, Richard
Publicado 2022

Crumble: reference free lossy compression of sequence quality values

por Bonfield, James K, McCarthy, Shane A, Durbin, Richard
Publicado 2019

Identifying and removing haplotypic duplication in primary genome assemblies

por Guan, Dengfeng, McCarthy, Shane A, Wood, Jonathan, Howe, Kerstin, Wang, Yadong, Durbin, Richard
Publicado 2020

Efficient iterative Hi-C scaffolder based on N-best neighbors

por Guan, Dengfeng, McCarthy, Shane A., Ning, Zemin, Wang, Guohua, Wang, Yadong, Durbin, Richard
Publicado 2021

Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors

por Guan, Dengfeng, McCarthy, Shane A., Ning, Zemin, Wang, Guohua, Wang, Yadong, Durbin, Richard
Publicado 2021

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

por Dolle, Dirk D., Liu, Zhicheng, Cotten, Matthew, Simpson, Jared T., Iqbal, Zamin, Durbin, Richard, McCarthy, Shane A., Keane, Thomas M.
Publicado 2017

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

por 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.
Publicado 2023

Twelve years of SAMtools and BCFtools

por 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
Publicado 2021

Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians

por 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
Publicado 2023

A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

por 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
Publicado 2021

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

por Yen, Eugenie C, McCarthy, Shane A, Galarza, Juan A, Generalovic, Tomas N, Pelan, Sarah, Nguyen, Petr, Meier, Joana I, Warren, Ian A, Mappes, Johanna, Durbin, Richard, Jiggins, Chris D
Publicado 2020

Correction to: A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

por Yen, Eugenie C, McCarthy, Shane A, Galarza, Juan A, Generalovic, Tomas N, Pelan, Sarah, Nguyen, Petr, Meier, Joana I, Warren, Ian A, Mappes, Johanna, Durbin, Richard, Jiggins, Chris D
Publicado 2021

The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861)

por 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
Publicado 2020

Whole-exome sequencing of 228 patients with sporadic Parkinson’s disease

por Sandor, Cynthia, Honti, Frantisek, Haerty, Wilfried, Szewczyk-Krolikowski, Konrad, Tomlinson, Paul, Evetts, Sam, Millin, Stephanie, Keane, Thomas, McCarthy, Shane A., Durbin, Richard, Talbot, Kevin, Hu, Michele, Webber, Caleb, Ponting, Chris P., Wade-Martins, Richard
Publicado 2017

The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens

por 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
Publicado 2021

The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788

por Mead, Dan, Fingland, Kathryn, Cripps, Rachel, Portela Miguez, Roberto, Smith, Michelle, Corton, Craig, Oliver, Karen, Skelton, Jason, Betteridge, Emma, Doulcan, Jale, Quail, Michael A., McCarthy, Shane A., Howe, Kerstin, Sims, Ying, Torrance, James, Tracey, Alan, Challis, Richard, Durbin, Richard, Blaxter, Mark
Publicado 2020

The gene-rich genome of the scallop Pecten maximus

por 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
Publicado 2020

The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758

por 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
Publicado 2021