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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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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MUMmer4: A fast and versatile genome alignment system von Marçais, Guillaume, Delcher, Arthur L, Phillippy, Adam M, Coston, Rachel, Salzberg, Steven L, Zimin, Aleksey

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Interactive metagenomic visualization in a Web browser von Ondov, Brian D, Bergman, Nicholas H, Phillippy, Adam M

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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries von Jain, Chirag, Rodriguez-R, Luis M., Phillippy, Adam M., Konstantinidis, Konstantinos T., Aluru, Srinivas

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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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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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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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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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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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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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The structure, function and evolution of a complete human chromosome 8 von Logsdon, Glennis A., Vollger, Mitchell R., Hsieh, PingHsun, Mao, Yafei, Liskovykh, Mikhail A., Koren, Sergey, Nurk, Sergey, Mercuri, Ludovica, Dishuck, Philip C., Rhie, Arang, de Lima, Leonardo G., Dvorkina, Tatiana, Porubsky, David, Harvey, William T., Mikheenko, Alla, Bzikadze, Andrey V., Kremitzki, Milinn, Graves-Lindsay, Tina A., Jain, Chirag, Hoekzema, Kendra, Murali, Shwetha C., Munson, Katherine M., Baker, Carl, Sorensen, Melanie, Lewis, Alexandra M., Surti, Urvashi, Gerton, Jennifer L., Larionov, Vladimir, Ventura, Mario, Miga, Karen H., Phillippy, Adam M., Eichler, Evan E.

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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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From telomere to telomere: The transcriptional and epigenetic state of human repeat elements von Hoyt, Savannah J, Storer, Jessica M, Hartley, Gabrielle A, Grady, Patrick G S, Gershman, Ariel, de Lima, Leonardo G, Limouse, Charles, Halabian, Reza, Wojenski, Luke, Rodriguez, Matias, Altemose, Nicolas, Rhie, Arang, Core, Leighton J, Gerton, Jennifer L, Makalowski, Wojciech, Olson, Daniel, Rosen, Jeb, Smit, Arian F A, Straight, Aaron F, Vollger, Mitchell R, Wheeler, Travis J, Schatz, Michael C, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Miga, Karen H, O'Neill, Rachel J

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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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GAGE: A critical evaluation of genome assemblies and assembly algorithms von Salzberg, Steven L, Phillippy, Adam M, Zimin, Aleksey, Puiu, Daniela, Magoc, Tanja, Koren, Sergey, Treangen, Todd J, Schatz, Michael C, Delcher, Arthur L, Roberts, Michael, Marçais, Guillaume, Pop, Mihai, Yorke, James A

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The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts von Liu, Zhanjiang, Liu, Shikai, Yao, Jun, Bao, Lisui, Zhang, Jiaren, Li, Yun, Jiang, Chen, Sun, Luyang, Wang, Ruijia, Zhang, Yu, Zhou, Tao, Zeng, Qifan, Fu, Qiang, Gao, Sen, Li, Ning, Koren, Sergey, Jiang, Yanliang, Zimin, Aleksey, Xu, Peng, Phillippy, Adam M., Geng, Xin, Song, Lin, Sun, Fanyue, Li, Chao, Wang, Xiaozhu, Chen, Ailu, Jin, Yulin, Yuan, Zihao, Yang, Yujia, Tan, Suxu, Peatman, Eric, Lu, Jianguo, Qin, Zhenkui, Dunham, Rex, Li, Zhaoxia, Sonstegard, Tad, Feng, Jianbin, Danzmann, Roy G., Schroeder, Steven, Scheffler, Brian, Duke, Mary V., Ballard, Linda, Kucuktas, Huseyin, Kaltenboeck, Ludmilla, Liu, Haixia, Armbruster, Jonathan, Xie, Yangjie, Kirby, Mona L., Tian, Yi, Flanagan, Mary Elizabeth, Mu, Weijie, Waldbieser, Geoffrey C.

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