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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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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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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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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Genetic variation in an individual human exome von Ng, Pauline C, Levy, Samuel, Huang, Jiaqi, Stockwell, Timothy B, Walenz, Brian P, Li, Kelvin, Axelrod, Nelson, Busam, Dana A, Strausberg, Robert L, Venter, J Craig

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Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation von Koren, Sergey, Walenz, Brian P, Berlin, Konstantin, Miller, Jason R, Bergman, Nicholas H, Phillippy, Adam M

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Effect of sequence depth and length in long-read assembly of the maize inbred NC358 von Ou, Shujun, Liu, Jianing, Chougule, Kapeel M., Fungtammasan, Arkarachai, Seetharam, Arun S., Stein, Joshua C., Llaca, Victor, Manchanda, Nancy, Gilbert, Amanda M., Wei, Sharon, Chin, Chen-Shan, Hufnagel, David E., Pedersen, Sarah, Snodgrass, Samantha J., Fengler, Kevin, Woodhouse, Margaret, Walenz, Brian P., Koren, Sergey, Phillippy, Adam M., Hannigan, Brett T., Dawe, R. Kelly, Hirsch, Candice N., Hufford, Matthew B., Ware, Doreen

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Nanoliter reactors improve multiple displacement amplification of genomes from single cells von Marcy, Yann, Ishoey, Thomas, Lasken, Roger S, Stockwell, Timothy B, Walenz, Brian P, Halpern, Aaron L, Beeson, Karen Y, Goldberg, Susanne M D, Quake, Stephen R

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The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning von Kim, Jung-Hyun, Noskov, Vladimir N., Ogurtsov, Aleksey Y., Nagaraja, Ramaiah, Petrov, Nikolai, Liskovykh, Mikhail, Walenz, Brian P., Lee, Hee-Sheung, Kouprina, Natalay, Phillippy, Adam M., Shabalina, Svetlana A., Schlessinger, David, Larionov, Vladimir

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Hybrid assembly with long and short reads improves discovery of gene family expansions von Miller, Jason R, Zhou, Peng, Mudge, Joann, Gurtowski, James, Lee, Hayan, Ramaraj, Thiruvarangan, Walenz, Brian P, Liu, Junqi, Stupar, Robert M, Denny, Roxanne, Song, Li, Singh, Namrata, Maron, Lyza G, McCouch, Susan R, McCombie, W Richard, Schatz, Michael C, Tiffin, Peter, Young, Nevin D, Silverstein, Kevin A T

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Telomere-to-telomere assembly of diploid chromosomes with Verkko von Rautiainen, Mikko, Nurk, Sergey, Walenz, Brian P., Logsdon, Glennis A., Porubsky, David, Rhie, Arang, Eichler, Evan E., Phillippy, Adam M., Koren, Sergey

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De novo assembly of haplotype-resolved genomes with trio binning von Koren, Sergey, Rhie, Arang, Walenz, Brian P, Dilthey, Alexander T, Bickhart, Derek M, Kingan, Sarah B, Hiendleder, Stefan, Williams, John L, Smith, Timothy P L, Phillippy, Adam M

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Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation von Formenti, Giulio, Rhie, Arang, Walenz, Brian P., Thibaud-Nissen, Françoise, Shafin, Kishwar, Koren, Sergey, Myers, Eugene W., Jarvis, Erich D., Phillippy, Adam M.

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An algorithm for automated closure during assembly von Koren, Sergey, Miller, Jason R, Walenz, Brian P, Sutton, Granger

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Aggressive assembly of pyrosequencing reads with mates von Miller, Jason R., Delcher, Arthur L., Koren, Sergey, Venter, Eli, Walenz, Brian P., Brownley, Anushka, Johnson, Justin, Li, Kelvin, Mobarry, Clark, Sutton, Granger

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The diploid genome sequence of an individual human von Levy, Samuel, Sutton, Granger, Ng, Pauline C, Feuk, Lars, Halpern, Aaron L, Walenz, Brian P, Axelrod, Nelson, Huang, Jiaqi, Kirkness, Ewen F, Denisov, Gennady, Lin, Yuan, MacDonald, Jeffrey R, Pang, Andy Wing Chun, Shago, Mary, Stockwell, Timothy B, Tsiamouri, Alexia, Bafna, Vineet, Bansal, Vikas, Kravitz, Saul A, Busam, Dana A, Beeson, Karen Y, McIntosh, Tina C, Remington, Karin A, Abril, Josep F, Gill, John, Borman, Jon, Rogers, Yu-Hui, Frazier, Marvin E, Scherer, Stephen W, Strausberg, Robert L, Venter, J Craig

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An improved genome assembly uncovers prolific tandem repeats in Atlantic cod von Tørresen, Ole K, Star, Bastiaan, Jentoft, Sissel, Reinar, William B, Grove, Harald, Miller, Jason R, Walenz, Brian P, Knight, James, Ekholm, Jenny M, Peluso, Paul, Edvardsen, Rolf B, Tooming-Klunderud, Ave, Skage, Morten, Lien, Sigbjørn, Jakobsen, Kjetill S, Nederbragt, Alexander J

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Improved reference genome for the domestic horse increases assembly contiguity and composition von Kalbfleisch, Theodore S., Rice, Edward S., DePriest, Michael S., Walenz, Brian P., Hestand, Matthew S., Vermeesch, Joris R., O′Connell, Brendan L., Fiddes, Ian T., Vershinina, Alisa O., Saremi, Nedda F., Petersen, Jessica L., Finno, Carrie J., Bellone, Rebecca R., McCue, Molly E., Brooks, Samantha A., Bailey, Ernest, Orlando, Ludovic, Green, Richard E., Miller, Donald C., Antczak, Douglas F., MacLeod, James N.

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A space-efficient construction of the Burrows-Wheeler transform for genomic data von Lippert, Ross A, Mobarry, Clark M, Walenz, Brian P

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