RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Export

@article{citeulike:5245930, abstract = {We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4x to 6x, despite having up to 42.2\% in exact repeats.}, author = {Wang, Jun and Wong, Gane Ka-Shu K. and Ni, Peixiang and Han, Yujun and Huang, Xiangang and Zhang, Jianguo and Ye, Chen and Zhang, Yong and Hu, Jianfei and Zhang, Kunlin and Xu, Xin and Cong, Lijuan and Lu, Hong and Ren, Xide and Ren, Xiaoyu and He, Jun and Tao, Lin and Passey, Douglas A. and Wang, Jian and Yang, Huanming and Yu, Jun and Li, Songgang}, citeulike-article-id = {5245930}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.165102}, citeulike-linkout-1 = {http://genome.cshlp.org/content/12/5/824.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/12/5/824.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/11997349}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=11997349}, day = {1}, doi = {10.1101/gr.165102}, issn = {1088-9051}, journal = {Genome research}, keywords = {assembler, assembly, mask, repeats, reps, software, tandem-repeats, tool}, month = {May}, number = {5}, pages = {824--831}, posted-at = {2009-09-28 15:42:47}, priority = {2}, title = {RePS: a sequence assembler that masks exact repeats identified from the shotgun data.}, url = {http://dx.doi.org/10.1101/gr.165102}, volume = {12}, year = {2002} }

TY - JOUR ID - citeulike:5245930 L3 - citeulike-article-id:5245930 N2 - We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4x to 6x, despite having up to 42.2% in exact repeats. IS - 5 JF - Genome research SN - 1088-9051 EP - 831 TI - RePS: a sequence assembler that masks exact repeats identified from the shotgun data. VL - 12 SP - 824 KW - assembler KW - assembly KW - mask KW - repeats KW - reps KW - software KW - tandem-repeats KW - tool AU - Wang, Jun AU - Wong, Gane Ka-Shu AU - Ni, Peixiang AU - Han, Yujun AU - Huang, Xiangang AU - Zhang, Jianguo AU - Ye, Chen AU - Zhang, Yong AU - Hu, Jianfei AU - Zhang, Kunlin AU - Xu, Xin AU - Cong, Lijuan AU - Lu, Hong AU - Ren, Xide AU - Ren, Xiaoyu AU - He, Jun AU - Tao, Lin AU - Passey, Douglas AU - Wang, Jian AU - Yang, Huanming AU - Yu, Jun AU - Li, Songgang PY - 2002/05/01/ UR - http://dx.doi.org/10.1101/gr.165102 ER -