Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies von Rhie, Arang, Walenz, Brian P., Koren, Sergey, Phillippy, Adam M.

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One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly von Koren, Sergey, Phillippy, Adam M

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HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads von Nurk, Sergey, Walenz, Brian P., Rhie, Arang, Vollger, Mitchell R., Logsdon, Glennis A., Grothe, Robert, Miga, Karen H., Eichler, Evan E., Phillippy, Adam M., Koren, Sergey

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The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes von Treangen, Todd J, Ondov, Brian D, Koren, Sergey, Phillippy, Adam M

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Hybrid error correction and de novo assembly of single-molecule sequencing reads von Koren, Sergey, Schatz, Michael C, Walenz, Brian P, Martin, Jeffrey, Howard, Jason T, Ganapathy, Ganeshkumar, Wang, Zhong, Rasko, David A, McCombie, W Richard, Jarvis, Erich D, Phillippy, Adam M

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Scaffolding of long read assemblies using long range contact information von Ghurye, Jay, Pop, Mihai, Koren, Sergey, Bickhart, Derek, Chin, Chen-Shan

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Integrating Hi-C links with assembly graphs for chromosome-scale assembly von Ghurye, Jay, Rhie, Arang, Walenz, Brian P, Schmitt, Anthony, Selvaraj, Siddarth, Pop, Mihai, Phillippy, Adam M, Koren, Sergey

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Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps von Dilthey, Alexander T., Jain, Chirag, Koren, Sergey, Phillippy, Adam M.

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Weighted minimizer sampling improves long read mapping von Jain, Chirag, Rhie, Arang, Zhang, Haowen, Chu, Claudia, Walenz, Brian P, Koren, Sergey, Phillippy, Adam M

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A fast adaptive algorithm for computing whole-genome homology maps von Jain, Chirag, Koren, Sergey, Dilthey, Alexander, Phillippy, Adam M, Aluru, Srinivas

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De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing von Schmidt, Maximilian H.-W., Vogel, Alexander, Denton, Alisandra K., Istace, Benjamin, Wormit, Alexandra, van de Geest, Henri, Bolger, Marie E., Alseekh, Saleh, Maß, Janina, Pfaff, Christian, Schurr, Ulrich, Chetelat, Roger, Maumus, Florian, Aury, Jean-Marc, Koren, Sergey, Fernie, Alisdair R., Zamir, Dani, Bolger, Anthony M., Usadel, Björn

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Mash Screen: high-throughput sequence containment estimation for genome discovery von Ondov, Brian D, Starrett, Gabriel J, Sappington, Anna, Kostic, Aleksandra, Koren, Sergey, Buck, Christopher B, Phillippy, Adam M

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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C von Kronenberg, Zev N., Rhie, Arang, Koren, Sergey, Concepcion, Gregory T., Peluso, Paul, Munson, Katherine M., Porubsky, David, Kuhn, Kristen, Mueller, Kathryn A., Low, Wai Yee, Hiendleder, Stefan, Fedrigo, Olivier, Liachko, Ivan, Hall, Richard J., Phillippy, Adam M., Eichler, Evan E., Williams, John L., Smith, Timothy P. L., Jarvis, Erich D., Sullivan, Shawn T., Kingan, Sarah B.

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RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification von Nasko, Daniel J, Koren, Sergey, Phillippy, Adam M, Treangen, Todd J

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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes von Shafin, Kishwar, Pesout, Trevor, Lorig-Roach, Ryan, Haukness, Marina, Olsen, Hugh E., Bosworth, Colleen, Armstrong, Joel, Tigyi, Kristof, Maurer, Nicholas, Koren, Sergey, Sedlazeck, Fritz J., Marschall, Tobias, Mayes, Simon, Costa, Vania, Zook, Justin M., Liu, Kelvin J., Kilburn, Duncan, Sorensen, Melanie, Munson, Katy M., Vollger, Mitchell R., Monlong, Jean, Garrison, Erik, Eichler, Evan E., Salama, Sofie, Haussler, David, Green, Richard E., Akeson, Mark, Phillippy, Adam, Miga, Karen H., Carnevali, Paolo, Jain, Miten, Paten, Benedict

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Epigenetic patterns in a complete human genome von Gershman, Ariel, Sauria, Michael E G, Guitart, Xavi, Vollger, Mitchell R, Hook, Paul W, Hoyt, Savannah J, Jain, Miten, Shumate, Alaina, Razaghi, Roham, Koren, Sergey, Altemose, Nicolas, Caldas, Gina V, Logsdon, Glennis A, Rhie, Arang, Eichler, Evan E, Schatz, Michael C, O'Neill, Rachel J, Phillippy, Adam M, Miga, Karen H, Timp, Winston

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A robust benchmark for detection of germline large deletions and insertions von Zook, Justin M., Hansen, Nancy F., Olson, Nathan D., Chapman, Lesley, Mullikin, James C., Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M., Boutros, Paul C., Sahraeian, Sayed Mohammad E., Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E., Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T., Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L., Bashir, Ali, Jackman, Shaun, Farrell, John J., Wenger, Aaron M., Alkan, Can, Soylev, Arda, Schatz, Michael C., Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C., Rosenfeld, Jeffrey A., Zhou, Weichen, Mills, Ryan E., Sage, Jay M., Davis, Jennifer R., Kaiser, Michael D., Oliver, John S., Catalano, Anthony P., Chaisson, Mark J. P., Spies, Noah, Sedlazeck, Fritz J., Salit, Marc

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Reply to ‘Errors in long-read assemblies can critically affect protein prediction’ von Koren, Sergey, Phillippy, Adam M., Simpson, Jared T., Loman, Nicholas J., Loose, Matthew

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HLALA—HLA typing from linearly projected graph alignments von Dilthey, Alexander T, Mentzer, Alexander J, Carapito, Raphael, Cutland, Clare, Cereb, Nezih, Madhi, Shabir A, Rhie, Arang, Koren, Sergey, Bahram, Seiamak, McVean, Gil, Phillippy, Adam M

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Bambus 2: scaffolding metagenomes von Koren, Sergey, Treangen, Todd J., Pop, Mihai

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