SimRAD: an R package for simulation‐based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches

Paul A Hohenlohe, Stephen J Amish, Julian M Catchen, Fred W Allendorf, Gordon Luikart, None, Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources. ,vol. 11, pp. 117- 122 ,(2011) , 10.1111/J.1755-0998.2010.02967.X

H. C. ROWE, S. RENAUT, A. GUGGISBERG, RAD in the realm of next-generation sequencing technologies. Molecular Ecology. ,vol. 20, pp. 3499- 3502 ,(2011) , 10.1111/J.1365-294X.2011.05197.X

Eckart Stolle, Robin F. A. Moritz, RESTseq – Efficient Benchtop Population Genomics with RESTriction Fragment SEQuencing PLoS ONE. ,vol. 8, pp. e63960- ,(2013) , 10.1371/JOURNAL.PONE.0063960

Jeremy Schmutz, Steven B. Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L. Hyten, Qijian Song, Jay J. Thelen, Jianlin Cheng, Dong Xu, Uffe Hellsten, Gregory D. May, Yeisoo Yu, Tetsuya Sakurai, Taishi Umezawa, Madan K. Bhattacharyya, Devinder Sandhu, Babu Valliyodan, Erika Lindquist, Myron Peto, David Grant, Shengqiang Shu, David Goodstein, Kerrie Barry, Montona Futrell-Griggs, Brian Abernathy, Jianchang Du, Zhixi Tian, Liucun Zhu, Navdeep Gill, Trupti Joshi, Marc Libault, Anand Sethuraman, Xue-Cheng Zhang, Kazuo Shinozaki, Henry T. Nguyen, Rod A. Wing, Perry Cregan, James Specht, Jane Grimwood, Dan Rokhsar, Gary Stacey, Randy C. Shoemaker, Scott A. Jackson, Genome sequence of the palaeopolyploid soybean Nature. ,vol. 463, pp. 178- 183 ,(2010) , 10.1038/NATURE08670

Robert J. Toonen, Jonathan B. Puritz, Zac H. Forsman, Jonathan L. Whitney, Iria Fernandez-Silva, Kimberly R. Andrews, Christopher E. Bird, ezRAD: a simplified method for genomic genotyping in non-model organisms PeerJ. ,vol. 1, ,(2013) , 10.7717/PEERJ.203

Christiaan V. Henkel, Erik Burgerhout, Daniëlle L. de Wijze, Ron P. Dirks, Yuki Minegishi, Hans J. Jansen, Herman P. Spaink, Sylvie Dufour, Finn-Arne Weltzien, Katsumi Tsukamoto, Guido E. E. J. M. van den Thillart, Primitive duplicate Hox clusters in the European eel's genome. PLOS ONE. ,vol. 7, pp. 32231- ,(2012) , 10.1371/JOURNAL.PONE.0032231

Humira Sonah, Maxime Bastien, Elmer Iquira, Aurélie Tardivel, Gaétan Légaré, Brian Boyle, Éric Normandeau, Jérôme Laroche, Stéphane Larose, Martine Jean, François Belzile, An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLOS ONE. ,vol. 8, ,(2013) , 10.1371/JOURNAL.PONE.0054603

Marcos De Donato, Sunday O. Peters, Sharon E. Mitchell, Tanveer Hussain, Ikhide G. Imumorin, Genotyping-by-Sequencing (GBS): A Novel, Efficient and Cost-Effective Genotyping Method for Cattle Using Next-Generation Sequencing PLoS ONE. ,vol. 8, pp. e62137- ,(2013) , 10.1371/JOURNAL.PONE.0062137

Martin Mascher, Shuangye Wu, Paul St. Amand, Nils Stein, Jesse Poland, Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley PLoS ONE. ,vol. 8, pp. e76925- ,(2013) , 10.1371/JOURNAL.PONE.0076925

Bing Zhang, Jinsong Xu, Zhikun Wu, Bo Wang, Haitao Li, Muhammad Younas, Lei Huang, Yingfeng Luo, Jiangsheng Wu, Songnian Hu, Kede Liu, Xun Chen, Xuemin Li, Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus BMC Genomics. ,vol. 14, pp. 346- 346 ,(2013) , 10.1186/1471-2164-14-346