An algorithm for automated closure during assembly

door Koren Sergey, Miller Jason R, Walenz Brian P, Sutton Granger
Gepubliceerd in 2010-09-01

An algorithm for automated closure during assembly

door Koren, Sergey, Miller, Jason R, Walenz, Brian P, Sutton, Granger
Gepubliceerd in 2010

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

door Rhie, Arang, Walenz, Brian P., Koren, Sergey, Phillippy, Adam M.
Gepubliceerd in Genome Biol (2020)

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

door Koren, Sergey, Walenz, Brian P., Berlin, Konstantin, Miller, Jason R., Bergman, Nicholas H., Phillippy, Adam M.
Gepubliceerd in Genome Res (2017)

Weighted minimizer sampling improves long read mapping

door Jain, Chirag, Rhie, Arang, Zhang, Haowen, Chu, Claudia, Walenz, Brian P, Koren, Sergey, Phillippy, Adam M
Gepubliceerd in Bioinformatics (2020)

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

door Ghurye, Jay, Rhie, Arang, Walenz, Brian P., Schmitt, Anthony, Selvaraj, Siddarth, Pop, Mihai, Phillippy, Adam M., Koren, Sergey
Gepubliceerd in PLoS Comput Biol (2019)

Aggressive assembly of pyrosequencing reads with mates

door Miller, Jason R., Delcher, Arthur L., Koren, Sergey, Venter, Eli, Walenz, Brian P., Brownley, Anushka, Johnson, Justin, Li, Kelvin, Mobarry, Clark, Sutton, Granger
Gepubliceerd in 2008

Nanoliter Reactors Improve Multiple Displacement Amplification of Genomes from Single Cells

door 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
Gepubliceerd in 2007

Genetic Variation in an Individual Human Exome

door 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
Gepubliceerd in 2008

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

door 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
Gepubliceerd in Genome Res (2020)

De novo assembly of haplotype-resolved genomes with trio binning

door 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.
Gepubliceerd in Nat Biotechnol (2018)

Hybrid error correction and de novo assembly of single-molecule sequencing reads

door Koren, Sergey, Schatz, Michael C., Walenz, Brian P., Martin, Jeffrey, Howard, Jason, Ganapathy, Ganeshkumar, Wang, Zhong, Rasko, David A., McCombie, W. Richard, Jarvis, Erich D., Phillippy, Adam M.
Gepubliceerd in 2012

The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning

door 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
Gepubliceerd in Sci Rep (2021)

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

door 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.
Gepubliceerd in BMC Genomics (2017)

Hybrid assembly with long and short reads improves discovery of gene family expansions

door 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.
Gepubliceerd in BMC Genomics (2017)

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

door 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
Gepubliceerd in Nat Commun (2020)

Improved reference genome for the domestic horse increases assembly contiguity and composition

door 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.
Gepubliceerd in Commun Biol (2018)

Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition

door 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.
Gepubliceerd in Commun Biol (2019)

The Diploid Genome Sequence of an Individual Human

door 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
Gepubliceerd in 2007

The Genome of Anopheles darlingi, the main neotropical malaria vector

door Marinotti, Osvaldo, Cerqueira, Gustavo C., de Almeida, Luiz Gonzaga Paula, Ferro, Maria Inês Tiraboschi, Loreto, Elgion Lucio da Silva, Zaha, Arnaldo, Teixeira, Santuza M. R., Wespiser, Adam R., Almeida e Silva, Alexandre, Schlindwein, Aline Daiane, Pacheco, Ana Carolina Landim, da Silva, Artur Luiz da Costa, Graveley, Brenton R., Walenz, Brian P., Lima, Bruna de Araujo, Ribeiro, Carlos Alexandre Gomes, Nunes-Silva, Carlos Gustavo, de Carvalho, Carlos Roberto, Soares, Célia Maria de Almeida, de Menezes, Claudia Beatriz Afonso, Matiolli, Cleverson, Caffrey, Daniel, Araújo, Demetrius Antonio M., de Oliveira, Diana Magalhães, Golenbock, Douglas, Grisard, Edmundo Carlos, Fantinatti-Garboggini, Fabiana, de Carvalho, Fabíola Marques, Barcellos, Fernando Gomes, Prosdocimi, Francisco, May, Gemma, de Azevedo Junior, Gilson Martins, Guimarães, Giselle Moura, Goldman, Gustavo Henrique, Padilha, Itácio Q. M., Batista, Jacqueline da Silva, Ferro, Jesus Aparecido, Ribeiro, José M. C., Fietto, Juliana Lopes Rangel, Dabbas, Karina Maia, Cerdeira, Louise, Agnez-Lima, Lucymara Fassarella, Brocchi, Marcelo, de Carvalho, Marcos Oliveira, Teixeira, Marcus de Melo, Diniz Maia, Maria de Mascena, Goldman, Maria Helena S., Cruz Schneider, Maria Paula, Felipe, Maria Sueli Soares, Hungria, Mariangela, Nicolás, Marisa Fabiana, Pereira, Maristela, Montes, Martín Alejandro, Cantão, Maurício E., Vincentz, Michel, Rafael, Miriam Silva, Silverman, Neal, Stoco, Patrícia Hermes, Souza, Rangel Celso, Vicentini, Renato, Gazzinelli, Ricardo Tostes, Neves, Rogério de Oliveira, Silva, Rosane, Astolfi-Filho, Spartaco, Maciel, Talles Eduardo Ferreira, Ürményi, Turán P., Tadei, Wanderli Pedro, Camargo, Erney Plessmann, de Vasconcelos, Ana Tereza Ribeiro
Gepubliceerd in 2013