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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy Lariviere, Delphine; Abueg, Linelle; Brajuka, Nadolina; Gallardo-Alba, Cristobal; Gruening, 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 Share Save
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City Wertheim, Joel O.; Wang, Jade C.; Leelawong, Mindy; Martin, Darren P.; Havens, Jennifer L.; Chowdhury, Moinuddin A.; Pekar, Jonathan E.; Amin, Helly; Arroyo, Anthony; Awandare, Gordon A.; Chow, Hoi Yan; Gonzalez, Edimarlyn; Luoma, Elizabeth; Morang'a, Collins M.; Nekrutenko, Anton; Shank, Stephen D.; Silver, Stefan; Quashie, Peter K.; Rakeman, Jennifer L.; Ruiz, Victoria; Torian, Lucia, V; Vasylyeva, Tetyana, I; Pond, Sergei L. Kosakovsky; Hughes, Scott Share Save
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function Martin, Darren P.; Lytras, Spyros; Lucaci, Alexander G.; Maier, Wolfgang; Gruening, Bjoern; Shank, Stephen D.; Weaver, Steven; MacLean, Oscar A.; Orton, Richard J.; Lemey, Philippe; Boni, Maciej F.; Tegally, Houriiyah; Harkins, Gordon W.; Scheepers, Cathrine; Bhiman, Jinal N.; Everatt, Josie; Amoako, Daniel G.; San, James Emmanuel; Giandhari, Jennifer; Sigal, Alex; Williamson, Carolyn; Hsiao, Nei-yuan; von Gottberg, Anne; De Klerk, Arne; Shafer, Robert W.; Robertson, David L.; Wilkinson, Robert J.; Sewell, B. Trevor; Lessells, Richard; Nekrutenko, Anton; Greaney, Allison J.; Starr, Tyler N.; Bloom, Jesse D.; Murrell, Ben; Wilkinson, Eduan; Gupta, Ravindra K.; de Oliveira, Tulio; Kosakovsky Pond, Sergei L. Share Save
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis Visualization, and Informatics Lab-space Schatz, Michael C.; Philippakis, Anthony A.; Afgan, Enis; Banks, Eric; Carey, Vincent J.; Carroll, Robert J.; Culotti, Alessandro; Ellrott, Kyle; Goecks, Jeremy; Grossman, Robert L.; Hall, Ira M.; Hansen, Kasper D.; Lawson, Jonathan; Leek, Jeffrey T.; Luria, Anne O'Donnell; Mosher, Stephen; Morgan, Martin; Nekrutenko, Anton; O'Connor, Brian D.; Osborn, Kevin; Paten, Benedict; Patterson, Candace; Tan, Frederick J.; Taylor, Casey Overby; Vessio, Jennifer; Waldron, Levi; Wang, Ting; Wuichet, Kristin Share Save
Ready-to-use public infrastructure for global SARS-CoV-2 monitoring Maier, Wolfgang; Bray, Simon; van den Beek, Marius; Bouvier, Dave; Coraor, Nathan; Miladi, Milad; Singh, Babita; De Argila, Jordi Rambla; Baker, Dannon; Roach, Nathan; Gladman, Simon; Coppens, Frederik; Martin, Darren P.; Lonie, Andrew; Gruening, Bjoern; Kosakovsky Pond, Sergei L.; Nekrutenko, Anton Share Save
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A single-cell RNA-sequencing training and analysis suite using the Galaxy framework Tekman, Mehmet; Batut, Berenice; Ostrovsky, Alexander; Antoniewski, Christophe; Clements, Dave; Ramirez, Fidel; Etherington, Graham J.; Hotz, Hans-Rudolf; Scholtalbers, Jelle; Manning, Jonathan R.; Bellenger, Lea; Doyle, Maria A.; Heydarian, Mohammad; Huang, Ni; Soranzo, Nicola; Moreno, Pablo; Mautner, Stefan; Papatheodorou, Irene; Nekrutenko, Anton; Taylor, James; Blankenberg, Daniel; Backofen, Rolf; Gruening, Bjoern Share Save
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update (vol 48, pg W395, 2020) Jalili, Vahid; Afgan, Enis; Gu, Qiang; Clements, Dave; Blankenberg, Daniel; Goecks, Jeremy; Taylor, James; Nekrutenko, Anton Share Save
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HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies Pond, Sergei L. Kosakovsky; Poon, Art F. Y.; Velazquez, Ryan; Weaver, Steven; Hepler, N. Lance; Murrell, Ben; Shank, Stephen D.; Magalis, Brittany Rife; Bouvier, Dave; Nekrutenko, Anton; Wisotsky, Sadie; Spielman, Stephanie J.; Frost, Simon D. W.; Muse, Spencer, V Share Save
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