title: RePS: a sequence assembler that masks exact repeats identified from the shotgun data.
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.
authors: Hangzhou Genomics Institute, Institute of Bioinformatics of Zhejiang University, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China. wangj@genomics.org.cn
authors: Jun
authors: J
authors: Wang
authors: Gane Ka-Shu
authors: GK
authors: Wong
authors: Peixiang
authors: P
authors: Ni
authors: Yujun
authors: Y
authors: Han
authors: Xiangang
authors: X
authors: Huang
authors: Jianguo
authors: J
authors: Zhang
authors: Chen
authors: C
authors: Ye
authors: Yong
authors: Y
authors: Zhang
authors: Jianfei
authors: J
authors: Hu
authors: Kunlin
authors: K
authors: Zhang
authors: Xin
authors: X
authors: Xu
authors: Lijuan
authors: L
authors: Cong
authors: Hong
authors: H
authors: Lu
authors: Xide
authors: X
authors: Ren
authors: Xiaoyu
authors: X
authors: Ren
authors: Jun
authors: J
authors: He
authors: Lin
authors: L
authors: Tao
authors: Douglas A
authors: DA
authors: Passey
authors: Jian
authors: J
authors: Wang
authors: Huanming
authors: H
authors: Yang
authors: Jun
authors: J
authors: Yu
authors: Songgang
authors: S
authors: Li
mesh_terms: D003001:Cloning, Molecular / Q000379:methods; D020451:Contig Mapping / Q000379:methods*; D006801:Humans; D012275:Oryza / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software