RT Journal
A1 Wang, Jun
A1 Wong, Gane Ka-Shu
A1 Ni, Peixiang
A1 Han, Yujun
A1 Huang, Xiangang
A1 Zhang, Jianguo
A1 Ye, Chen
A1 Zhang, Yong
A1 Hu, Jianfei
A1 Zhang, Kunlin
A1 Xu, Xin
A1 Cong, Lijuan
A1 Lu, Hong
A1 Ren, Xide
A1 Ren, Xiaoyu
A1 He, Jun
A1 Tao, Lin
A1 Passey, Douglas A.
A1 Wang, Jian
A1 Yang, Huanming
A1 Yu, Jun
A1 Li, Songgang
T1 
RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data
JF Genome Research 
JO Genome Research 
YR 2002 
FD May 01 
VO 12 
IS 5 
SP 824 
OP 831 
DO 10.1101/gr.165102 
UL http://genome.cshlp.org/content/12/5/824.abstract 
AB 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 Phrap 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 4× to 6×, despite having up to 42.2% in exact repeats.[The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: P. Green and A.F. Smit.]