<tt>RePS: </tt>A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data
Jun Wang(Chinese Academy of Sciences), Gane Ka‐Shu Wong(Chinese Academy of Sciences), Peixiang Ni(Chinese Academy of Sciences), Yujun Han(Chinese Academy of Sciences), Xiangang Huang(Chinese Academy of Sciences), Jianguo Zhang(Chinese Academy of Sciences), Chen Ye(Chinese Academy of Sciences), Yong Zhang(Chinese Academy of Sciences), Jianfei Hu(Chinese Academy of Sciences), Kunlin Zhang(Chinese Academy of Sciences), Xin Xu(Chinese Academy of Sciences), Lijuan Cong(Chinese Academy of Sciences), Hong Lü(Chinese Academy of Sciences), Xide Ren(Chinese Academy of Sciences), Xiaoyu Ren(Chinese Academy of Sciences), Jun He(Chinese Academy of Sciences), Lin Tao(Chinese Academy of Sciences), Douglas A. Passey(Chinese Academy of Sciences), Jian Wang(Chinese Academy of Sciences), Huanming Yang(Chinese Academy of Sciences), Jun Yu(Chinese Academy of Sciences), Songgang Li(Chinese Academy of Sciences)
Cited by 72Open Access
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 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 [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: P. Green and A.F. Smit.]
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