Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs von Colquhoun, Rachel M, Hall, Michael B, Lima, Leandro, Roberts, Leah W, Malone, Kerri M, Hunt, Martin, Letcher, Brice, Hawkey, Jane, George, Sophie, Pankhurst, Louise, Iqbal, Zamin

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Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M, Nguyen, Giang, Hall, Michael B, Colquhoun, Rachel M, Lima, Leandro, Schatz, Michael C, Ramakrishnan, Srividya, Iqbal, Zamin

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CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance von Nicholls, Samuel M, Poplawski, Radoslaw, Bull, Matthew J, Underwood, Anthony, Chapman, Michael, Abu-Dahab, Khalil, Taylor, Ben, Colquhoun, Rachel M, Rowe, Will P M, Jackson, Ben, Hill, Verity, O'Toole, Áine, Rey, Sara, Southgate, Joel, Amato, Roberto, Livett, Rich, Gonçalves, Sónia, Harrison, Ewan M, Peacock, Sharon J, Aanensen, David M, Rambaut, Andrew, Connor, Thomas R, Loman, Nicholas J

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Phylogenomic early warning signals for SARS-CoV-2 epidemic waves von Drake, Kieran O., Boyd, Olivia, Franceschi, Vinicius B., Colquhoun, Rachel M., Ellaby, Nicholas A.F., Volz, Erik M.

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Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity von Thomson, Emma C., Rosen, Laura E., Shepherd, James G., Spreafico, Roberto, da Silva Filipe, Ana, Wojcechowskyj, Jason A., Davis, Chris, Piccoli, Luca, Pascall, David J., Dillen, Josh, Lytras, Spyros, Czudnochowski, Nadine, Shah, Rajiv, Meury, Marcel, Jesudason, Natasha, De Marco, Anna, Li, Kathy, Bassi, Jessica, O’Toole, Aine, Pinto, Dora, Colquhoun, Rachel M., Culap, Katja, Jackson, Ben, Zatta, Fabrizia, Rambaut, Andrew, Jaconi, Stefano, Sreenu, Vattipally B., Nix, Jay, Zhang, Ivy, Jarrett, Ruth F., Glass, William G., Beltramello, Martina, Nomikou, Kyriaki, Pizzuto, Matteo, Tong, Lily, Cameroni, Elisabetta, Croll, Tristan I., Johnson, Natasha, Di Iulio, Julia, Wickenhagen, Arthur, Ceschi, Alessandro, Harbison, Aoife M., Mair, Daniel, Ferrari, Paolo, Smollett, Katherine, Sallusto, Federica, Carmichael, Stephen, Garzoni, Christian, Nichols, Jenna, Galli, Massimo, Hughes, Joseph, Riva, Agostino, Ho, Antonia, Schiuma, Marco, Semple, Malcolm G., Openshaw, Peter J.M., Fadda, Elisa, Baillie, J. Kenneth, Chodera, John D., Rihn, Suzannah J., Lycett, Samantha J., Virgin, Herbert W., Telenti, Amalio, Corti, Davide, Robertson, David L., Snell, Gyorgy

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Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic von Jackson, Ben, Boni, Maciej F., Bull, Matthew J., Colleran, Amy, Colquhoun, Rachel M., Darby, Alistair C., Haldenby, Sam, Hill, Verity, Lucaci, Anita, McCrone, John T., Nicholls, Samuel M., O’Toole, Áine, Pacchiarini, Nicole, Poplawski, Radoslaw, Scher, Emily, Todd, Flora, Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Loman, Nicholas J., Connor, Thomas R., Robertson, David L., Pybus, Oliver G., Rambaut, Andrew

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Phylogenomic early warning signals for SARS-CoV-2 epidemic wavesResearch in context von Kieran O. Drake, Olivia Boyd, Vinicius B. Franceschi, Rachel M. Colquhoun, Nicholas A.F. Ellaby, Erik M. Volz

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Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity von Thomson, Emma C, Rosen, Laura E, Shepherd, James G, Spreafico, Roberto, da Silva Filipe, Ana, Wojcechowskyj, Jason A, Davis, Chris, Piccoli, Luca, Pascall, David J, Dillen, Josh, Lytras, Spyros, Czudnochowski, Nadine, Shah, Rajiv, Meury, Marcel, Jesudason, Natasha, De Marco, Anna, Li, Kathy, Bassi, Jessica, O'Toole, Aine, Pinto, Dora, Colquhoun, Rachel M, Culap, Katja, Jackson, Ben, Zatta, Fabrizia, Rambaut, Andrew, Jaconi, Stefano, Sreenu, Vattipally B, Nix, Jay, Zhang, Ivy, Jarrett, Ruth F, Glass, William G, Beltramello, Martina, Nomikou, Kyriaki, Pizzuto, Matteo, Tong, Lily, Cameroni, Elisabetta, Croll, Tristan I, Johnson, Natasha, Di Iulio, Julia, Wickenhagen, Arthur, Ceschi, Alessandro, Harbison, Aoife M, Mair, Daniel, Ferrari, Paolo, Smollett, Katherine, Sallusto, Federica, Carmichael, Stephen, Garzoni, Christian, Nichols, Jenna, Galli, Massimo, Hughes, Joseph, Riva, Agostino, Ho, Antonia, Schiuma, Marco, Semple, Malcolm G, Openshaw, Peter JM, Fadda, Elisa, Baillie, J Kenneth, Chodera, John D, ISARIC4C Investigators, COVID-19 Genomics UK (COG-UK) Consortium, Rihn, Suzannah J, Lycett, Samantha J, Virgin, Herbert W, Telenti, Amalio, Corti, Davide, Robertson, David L, Snell, Gyorgy

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Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic von Jackson, Ben, Boni, Maciej F, Bull, Matthew J, Colleran, Amy, Colquhoun, Rachel M, Darby, Alistair C, Haldenby, Sam, Hill, Verity, Lucaci, Anita, McCrone, John T, Nicholls, Samuel M, O'Toole, Áine, Pacchiarini, Nicole, Poplawski, Radoslaw, Scher, Emily, Todd, Flora, Webster, Hermione J, Whitehead, Mark, Wierzbicki, Claudia, COVID-19 Genomics UK (COG-UK) Consortium, Loman, Nicholas J, Connor, Thomas R, Robertson, David L, Pybus, Oliver G, Rambaut, Andrew

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CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance von Nicholls, Samuel M, Poplawski, Radoslaw, Bull, Matthew J, Underwood, Anthony, Chapman, Michael, Abu-Dahab, Khalil, Taylor, Ben, Colquhoun, Rachel M, Rowe, Will PM, Jackson, Ben, Hill, Verity, O’Toole, Áine, Rey, Sara, Southgate, Joel, Amato, Roberto, Livett, Rich, Gonçalves, Sónia, Harrison, Ewan M, Peacock, Sharon J, Aanensen, David M, Rambaut, Andrew, Connor, Thomas R, Loman, Nicholas J, The COVID-19 Genomics UK (COG-UK) Consortium

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Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity von Volz, Erik, Hill, Verity, McCrone, John T, Price, Anna, Jorgensen, David, O'Toole, Áine, Southgate, Joel, Johnson, Robert, Jackson, Ben, Nascimento, Fabricia F, Rey, Sara M, Nicholls, Samuel M, Colquhoun, Rachel M, da Silva Filipe, Ana, Shepherd, James, Pascall, David J, Shah, Rajiv, Jesudason, Natasha, Li, Kathy, Jarrett, Ruth, Pacchiarini, Nicole, Bull, Matthew, Geidelberg, Lily, Siveroni, Igor, COG-UK Consortium, Goodfellow, Ian, Loman, Nicholas J, Pybus, Oliver G, Robertson, David L, Thomson, Emma C, Rambaut, Andrew, Connor, Thomas R

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Additional file 6 of Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya, Iqbal, Zamin

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Additional file 4 of Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya, Iqbal, Zamin

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Additional file 11 of Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya, Iqbal, Zamin

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Additional file 3 of Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya, Iqbal, Zamin

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Additional file 5 of Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya, Iqbal, Zamin

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Additional file 12 of Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya, Iqbal, Zamin

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Additional file 14 of Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya, Iqbal, Zamin

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Additional file 9 of Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya, Iqbal, Zamin

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Additional file 8 of Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes von Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya, Iqbal, Zamin

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