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HGGA: hierarchical guided genome assembler
BMC Bioinformatics, 2022 AbstractBackgroundDe novogenome assembly typically produces a set of contigs instead of the complete genome. Thus additional data such as genetic linkage maps, optical maps, or Hi-C data is needed to resolve the complete structure of the genome. Most of the previous work uses the additional data to order and orient contigs.ResultsHere we introduce a ...Riku Walve, Leena Salmelaopenaire +5 more sourcesAssembler for de novo assembly of large genomes [PDF]
Proceedings of the National Academy of Sciences, 2013 Significance Assembling a large genome faces three challenges: assembly quality, computer memory requirement, and execution time. Our developed assembler, JR-Assembler, uses ( a ) a strategy that selects good seeds for contig construction, ( b Te-Chin, Chu, Chen-Hua, Lu, Tsunglin, Liu, Greg C, Lee, Wen-Hsiung, Li, Arthur Chun-Chieh, Shih +5 moreopenaire +2 more sourcesA chromosome scale assembly of the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), genome
BMC Research Notes, 2023 Objective The tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae), is a pest damaging many cultivated crops in North America.O. P. Perera, Surya Saha, James Glover, Katherine A. Parys, K. Clint Allen, Snejana Grozeva, Ryan Kurtz, Gadi V. P. Reddy, J. Spencer Johnston, Mark Daly, Thomas Swale +10 moredoaj +1 more sourceShort read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance [PDF]
, 2011 Background: Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms.Wheat, Christopher W., Markus Pfenninger, Rotter, Björn, Pfenninger, Markus, Björn Rotter, Christopher W Wheat, Nicolas Krezdorn, Feldmeyer, Barbara, Krezdorn, Nicolas, Rotter, Bjoern, Barbara Feldmeyer, Feldmeyer Barbara, Pfenninger Markus, Krezdorn Nicolas, Rotter Björn, Wheat Christopher W +15 morecore +2 more sourcesComparison of whole genome assemblies of the human genome [PDF]
Nucleic Acids Research, 2002 A fundamental problem in the human genome project is uncovering the correct assembly of the human genome. Many studies, including transcriptional analysis, SNP detection and characterization, gene finding and EST clustering, use genome assemblies as templates so it is important to determine the consistency among the various whole genome assemblies.Eric C, Rouchka, Warren, Gish, David J, States +2 moreopenaire +2 more sourcesChromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential
Nature Genetics, 2021 Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding.M. Rabanus-Wallace, B. Hackauf, M. Mascher, Thomas M. Lux, T. Wicker, H. Gundlach, M. Báez, A. Houben, K. Mayer, Liang-Liang Guo, J. Poland, C. Pozniak, S. Walkowiak, J. Melonek, C. Praz, M. Schreiber, H. Budak, Matthias Heuberger, B. Steuernagel, B. Wulff, A. Börner, Brook Byrns, J. Čížková, D. Fowler, A. Fritz, A. Himmelbach, G. Kaithakottil, J. Keilwagen, B. Keller, David J F Konkin, J. Larsen, Qiang Li, B. Myśków, S. Padmarasu, Nidhi Rawat, Uğur Sesiz, Sezgi Biyiklioglu-Kaya, A. Sharpe, H. Šimková, I. Small, D. Swarbreck, Helena Toegelová, N. Tsvetkova, A. Voylokov, J. Vrána, E. Bauer, Hanna Bolibok-Brągoszewska, J. Doležel, Anthony Hall, J. Jia, V. Korzun, A. Laroche, Xue-Feng Ma, F. Ordon, H. Özkan, M. Rakoczy-Trojanowska, U. Scholz, A. Schulman, Dörthe Siekmann, S. Stojałowski, V. Tiwari, M. Spannagl, N. Stein +62 moresemanticscholar +1 more sourceMulti-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis [PDF]
, 2010 A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo).Kent M Reed, Zhang, Liqing, Zhang Hong-Bin, Kim, Heebal, Rami A Dalloul, Langenberger, D., Scheuring, C., Evans, Clive, Crooijmans, R. P. M. A., Lee, Mi-Kyung, Lee, Taeheon, Kim, H., Evans, C., Nefedov Mikhail, Mane, Shrinivasrao, Frederickson, K. M., Crooijmans, Richard P. M. A., Williams, K. P., Marz, M., Liqing Zhang, Paul Flicek, Dodgson, J. B., David Langenberger, Smith Jacqueline, Dodgson, J. B., Flicek, Paul, Dong, J. J., Jiang, A., Kim, K. W., Zhang Yang, Kim, H., Manja Marz, Long, J. A., Williams, Kelly P., Schatz Michael C., Julie A. Long, Raineri Emanuele, Folkerts, O., Otto Folkerts, McElroy, A. P., Zhang, L., Delany, Mary E., Long, Julie A., Kelly P. Williams, McElroy Audrey P., Paton, I. R., Beal Kathryn, de Jong, P., Vilella, A. J., Yorke, J. A., Vilella Albert J., Salzberg, Steven L., Harkins Tim T., Kim Sungwon, Crasta Oswald, Burt, David W., Bouffard Pascal, Schroeder, S., Albert J. Vilella, Burt, D. W., Liliana Florea, Mane Shrinivasrao, Carl J. Schmidt, Modise, Thero, Harkins, T. T., Jacqueline Smith, Frederickson, Karin M., Kristal Cooper, Stadler Peter F., Martien A. M. Groenen, Steven L. Salzberg, van Tassell, C. P., Smith, E. J., Blomberg, L. A., Modise, T., Tafer, Hakim, Schmidt, C. J., William S Payne, Dong, Jennifer J., Florea Liliana, Vilella, A. J., Notredame, C., Lee, M. K., Kathryn Beal, Jiang, A., Bouffard, Pascal, Geo Pertea, Mi-Kyung Lee, Mane, S., Roberts, Richard J., Delany, M. E., Jerry B. Dodgson, Schmidt, Carl J., Pertea, Geo, Searle Stephen M. J., Williams, K. P., Frederickson Karin M., Beal, K., Tim T Harkins, Lee, T., Langenberger, David, Searle, S. M. J., Ruffier, M., Puiu, D., Dalloul, R. A., Van Tassell, C. P., Schatz, M. C., Julie A Long, Jennifer J Dong, Raineri, E., Modise Thero, Long Julie A., Reed, Kent M., De, Supriyo, Oswald Crasta, Zimin, Aleksey V., Folkerts, O., Zhang, Y., Schroeder Steven, Roger A Coulombe, Hoffmann Steve, Crasta, Oswald, McElroy, Audrey P., Tu, Zhijian Jake, Florea, L., Magali Ruffier, Curtis P. Van Tassell, Williams Kelly P., William S. Payne, Megens, H. J., Zhang, X., Bouffard, P., James A Yorke, Kaiser, Pete, Daniela Puiu, Stephen M. J. Searle, Modise, T., Notredame Cédric, Hoffmann, Steve, Ruffier Magali, Taeheon Lee, Guillaume Marcais, Evans Clive, Le Ann Blomberg, Qioa, Dan, Herrero Javier, Zhang Liqing, Crooijmans, R. P., Evans, C., Prickett, Dennis, Groenen, M. A., Cooper, K., Tu, Z. J., Dalloul, R.A., De Supriyo, Kaiser, P., Schmidt, C. J., Van Tassell Curtis P., Tafer, H., Megens, Hendrik-Jan, Mane, Shrinivasrao P., Tafer, H., Marcais, G., Xiaojun Zhang, Crasta, O., Kyu-Won Kim, Dodgson Jerry B., Aleksey V. Zimin, Reed, K. M., Steve Hoffmann, Tu, Zhijian (Jake), Dalloul, Rami A., Ann Blomberg Le, Hoffmann, S., Zhang, Yang, David W Burt, Kent M. Reed, Pieter de Jong, Aslam, Luqman, Marz, M., Groenen, Martien A. M., Michael C Schatz, Zhijian Jake Tu, Burt David W., Pascal Bouffard, Pertea Geo, Richard P M A Crooijmans, Audrey P. McElroy, David W. Burt, Sonstegard, T. S., Marcais, G., Hakim Tafer, Smith, J., Zhang, H. B., Ruffier, Magali, Mikhail Nefedov, Albert J Vilella, Megens Hendrik-Jan, Clive Evans, Hendrik-Jan Megens, Kaiser Pete, Dennis Prickett, Puiu Daniela, Dan Qioa, Schroeder, S., Zhang, Hong-Bin, Zhang, Xiaojun, Audrey P McElroy, Zimin Aleksey V., Vilella, Albert J., Groenen, M. A. M., Martien A M Groenen, Coulombe, R. A., Supriyo De, Scheuring, C., Qioa, D., Nefedov, M., de Jong Pieter, McElroy, A. P., Folkerts, Otto, Yorke James A., Harkins, Tim T., Rami A. Dalloul, Zhijian (Jake) Tu, Lee Taeheon, Crooijmans, R.P.M.A., Searle, S. M., Megens, H. J., Edward J. Smith, Paton Ian R., Salzberg, S. L., Aleksey V Zimin, Cooper Kristal, Ian R. Paton, Emanuele Raineri, Langenberger David, Tu Zhijian (Jake), Long, J. A., Qioa, D., Coulombe, R. A., Pete Kaiser, Aslam Luqman, Mane, S., Delany, M. E., Schatz, M. C., Sonstegard Tad S., Marz, Manja, Payne, William S., Carl J Schmidt, Andrew Jiang, Tu, Z., James A. Yorke, Long, J.A., Kelly P Williams, Lee, T., Edward J Smith, Notredame, Cédric, Stadler, P. F., Aslam, L., Prickett Dennis, Zimin, A. V., Herrero, J., Burt, D. W., Luqman Aslam, Crasta, O., Langenberger, D., Kaiser, P., Stadler, P. F., Van Tassell, Curtis P., Schmidt Carl J., Sonstegard, Tad S., Marz Manja, Lee, M. K., Puiu, Daniela, Marcais Guillaume, Crooijmans Richard P. M. A., Blomberg, Le Ann, Groenen Martien A. M., de Jong, P., Ruffier, M., Tad S. Sonstegard, Dalloul, R. A., Jiang Andrew, Frederickson, K. M., Florea, Liliana, Aslam, M.L., Smith Edward J., de Jong, Pieter, Cédric Notredame, Kim, K. W., Searle, Stephen M. J., Smith, Jacqueline, Harkins, T. T., Smith, Edward J., Karin M Frederickson, Chantel Scheuring, Marcais, Guillaume, Dalloul Rami A., Curtis P Van Tassell, Kim, Kyu-Won, Kim, S., Mary E Delany, Hong-Bin Zhang, Michael C. Schatz, Scheuring, Chantel, Kim Kyu-Won, Jiang, Andrew, Payne, W. S., Folkerts Otto, Zhang, H. B., Zimin, A. V., Schroeder, Steven, Yorke, J. A., Megens, H.J.W.C., Heebal Kim, Payne, W. S., Ann Blomberg, Le, Beal, K., Smith, Jacqueline; id_orcid, Puiu, D., Reed, K. M., Qioa Dan, Notredame, C., Pertea, G., Stephen M J Searle, Zhang Xiaojun, Prickett, D., Flicek, P., Salzberg, S. L., Karin M. Frederickson, Florea, L., Coulombe, Roger A., Smith, E. J., Delany Mary E., Scheuring Chantel, Sungwon Kim, Salzberg Steven L., Aslam, L., Jerry B Dodgson, Yang Zhang, Yorke, James A., Raineri, Emanuele, Paton, I. R., Bouffard, P., Tafer Hakim, Cooper, K., Dong, J. J., Nefedov, Mikhail, Kim Heebal, Cooper, Kristal, Roger A. Coulombe, Tim T. Harkins, Tad S Sonstegard, De, S., Nefedov, M., Herrero, Javier, Mary E. Delany, Raineri, E., Zhang, L., Hoffmann, S., De, S., Peter F Stadler, Kim, Sungwon, Zhang, X., Thero Modise, Beal, Kathryn, Sonstegard, T. S., Richard P. M. A. Crooijmans, Prickett, D., Steven Schroeder, Payne William S., Jennifer J. Dong, Groenen, M., Ann Blomberg, L., Lee Mi-Kyung, Zhang, Y., Flicek, P., Zimin, A.V., Dong Jennifer J., Schatz, Michael C., Coulombe Roger A., Peter F. Stadler, Flicek Paul, Javier Herrero, Paton, Ian R., Herrero, J., Ian R Paton, Dodgson, Jerry B., Steven L Salzberg, Shrinivasrao Mane, Stadler, Peter F., Pertea, G., Reed Kent M., et al., Stadler, P.F. +394 morecore +1 more source
