The nf-core framework for community-curated bioinformatics pipelines von Ewels, Philip A., Peltzer, Alexander, Fillinger, Sven, Patel, Harshil, Alneberg, Johannes, Wilm, Andreas, Garcia, Maxime Ulysse, Di Tommaso, Paolo, Nahnsen, Sven

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MultiQC: summarize analysis results for multiple tools and samples in a single report von Ewels, Philip, Magnusson, Måns, Lundin, Sverker, Käller, Max

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A Complete Overhaul of the Electron Energy-Loss Spectroscopy and X-Ray Absorption Spectroscopy Database: eelsdb.eu von Ewels, Philip, Sikora, Thierry, Serin, Virginie, Ewels, Chris P., Lajaunie, Luc

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Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C von Mifsud, Borbala, Tavares-Cadete, Filipe, Young, Alice N, Sugar, Robert, Schoenfelder, Stefan, Ferreira, Lauren, Wingett, Steven W, Andrews, Simon, Grey, William, Ewels, Philip A, Herman, Bram, Happe, Scott, Higgs, Andy, LeProust, Emily, Follows, George A, Fraser, Peter, Luscombe, Nicholas M, Osborne, Cameron S

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Global Reorganization of the Nuclear Landscape in Senescent Cells von Chandra, Tamir, Ewels, Philip Andrew, Schoenfelder, Stefan, Furlan-Magaril, Mayra, Wingett, Steven William, Kirschner, Kristina, Thuret, Jean-Yves, Andrews, Simon, Fraser, Peter, Reik, Wolf

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HiCUP: pipeline for mapping and processing Hi-C data [version 1; peer review: 2 approved, 1 approved with reservations] von Wingett, Steven W, Ewels, Philip, Furlan-Magaril, Mayra, Nagano, Takashi, Schoenfelder, Stefan, Fraser, Peter, Andrews, Simon

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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 1; peer review: 2 approved] von Garcia, Maxime, Juhos, Szilveszter, Larsson, Malin, Olason, Pall I, Martin, Marcel, Eisfeldt, Jesper, DiLorenzo, Sebastian, Sandgren, Johanna, Díaz De Ståhl, Teresita, Ewels, Philip, Wirta, Valtteri, Nistér, Monica, Käller, Max, Nystedt, Björn

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Ten simple rules for making a software tool workflow-ready von Brack, Paul, Crowther, Peter, Soiland-Reyes, Stian, Owen, Stuart, Lowe, Douglas, Williams, Alan R, Groom, Quentin, Dillen, Mathias, Coppens, Frederik, Grüning, Björn, Eguinoa, Ignacio, Ewels, Philip, Goble, Carole

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Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes von Wojewodzic, Marcin W., Leithaug, Magnus, Lauritzen, Marianne, Lyle, Robert, Haglund, Sofia, Rubin, Carl-Johan, Ewels, Philip A., Grotmol, Tom, Rounge, Trine B.

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Cluster Flow: A user-friendly bioinformatics workflow tool [version 1; peer review: 3 approved] von Ewels, Philip, Krueger, Felix, Käller, Max, Andrews, Simon

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High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia von Baker, Stephen, Holt, Kathryn, van de Vosse, Esther, Roumagnac, Philippe, Whitehead, Sally, King, Emma, Ewels, Philip, Keniry, Andrew, Weill, François-Xavier, Lightfoot, Diane, van Dissel, Jaap T, Sanderson, Kenneth E, Farrar, Jeremy, Achtman, Mark, Deloukas, Panagiotis, Dougan, Gordon

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Cluster Flow: A user-friendly bioinformatics workflow tool [version 2; peer review: 3 approved] von Ewels, Philip, Krueger, Felix, Käller, Max, Andrews, Simon

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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved] von Garcia, Maxime, Juhos, Szilveszter, Larsson, Malin, Olason, Pall I, Martin, Marcel, Eisfeldt, Jesper, DiLorenzo, Sebastian, Sandgren, Johanna, Díaz De Ståhl, Teresita, Ewels, Philip, Wirta, Valtteri, Nistér, Monica, Käller, Max, Nystedt, Björn

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Meet the neighbours: tools to dissect nuclear structure and function von Osborne, Cameron S, Ewels, Philip A, Young, Alice N C

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Linked‐read sequencing enables haplotype‐resolved resequencing at population scale von Lutgen, Dave, Ritter, Raphael, Olsen, Remi‐André, Schielzeth, Holger, Gruselius, Joel, Ewels, Philip, García, Jesús T., Shirihai, Hadoram, Schweizer, Manuel, Suh, Alexander, Burri, Reto

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Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies von Patalano, Solenn, Vlasova, Anna, Wyatt, Chris, Ewels, Philip, Camara, Francisco, Ferreira, Pedro G., Asher, Claire L., Jurkowski, Tomasz P., Segonds-Pichon, Anne, Bachman, Martin, González-Navarrete, Irene, Minoche, André E., Krueger, Felix, Lowy, Ernesto, Marcet-Houben, Marina, Rodriguez-Ales, Jose Luis, Nascimento, Fabio S., Balasubramanian, Shankar, Gabaldon, Toni, Tarver, James E., Andrews, Simon, Himmelbauer, Heinz, Hughes, William O. H., Guigó, Roderic, Reik, Wolf, Sumner, Seirian

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Understanding functional miRNA–target interactions in vivo by site-specific genome engineering von Bassett, Andrew R., Azzam, Ghows, Wheatley, Lucy, Tibbit, Charlotte, Rajakumar, Timothy, McGowan, Simon, Stanger, Nathan, Ewels, Philip Andrew, Taylor, Stephen, Ponting, Chris P., Liu, Ji-Long, Sauka-Spengler, Tatjana, Fulga, Tudor A.

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A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements von Arnqvist, Göran, Westerberg, Ivar, Galbraith, James, Sayadi, Ahmed, Scofield, Douglas G, Olsen, Remi-André, Immonen, Elina, Bonath, Franziska, Ewels, Philip, Suh, Alexander

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Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease von Ouwehand, Willem, Keniry, Andrew, Fisher, Sheila A, Jewell, Derek P, Anderson, Carl A, Prescott, Natalie J, Deloukas, Panos, Blaszczyk, Katarzyna, Mansfield, John C, Mathew, Christopher G, Watkins, Nick, Drummond, Hazel, Cummings, Fraser R, Forbes, Alastair, Barrett, Jeffrey C, Ravindrarajah, Radhi, Sanderson, Jeremy, Inouye, Mike, Hunt, Sarah, Nimmo, Elaine R, Johnson, Christopher, Bumpstead, Suzannah, Hanson, Catherine E, Lobo, Alan, Massey, Dunecan, Cardon, Lon, Ewels, Philip, Satsangi, Jack, Tremelling, Mark, Gwilliam, Rhian, Carter, Martyn, Berzuini, Carlo, Lees, Charlie W, Onnie, Clive M, Parkes, Miles, Lewis, Cathryn M

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Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women von Engström, Karin, Wojdacz, Tomasz K., Marabita, Francesco, Ewels, Philip, Käller, Max, Vezzi, Francesco, Prezza, Nicola, Gruselius, Joel, Vahter, Marie, Broberg, Karin

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