RePS: a sequence assembler that masks exact repeats identified from the shotgun data.
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.
Wang
Jun
J
Hangzhou Genomics Institute, Institute of Bioinformatics of Zhejiang University, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China. wangj@genomics.org.cn
Wong
Gane Ka-Shu
GK
Ni
Peixiang
P
Han
Yujun
Y
Huang
Xiangang
X
Zhang
Jianguo
J
Ye
Chen
C
Zhang
Yong
Y
Hu
Jianfei
J
Zhang
Kunlin
K
Xu
Xin
X
Cong
Lijuan
L
Lu
Hong
H
Ren
Xide
X
Ren
Xiaoyu
X
He
Jun
J
Tao
Lin
L
Passey
Douglas A
DA
Wang
Jian
J
Yang
Huanming
H
Yu
Jun
J
Li
Songgang
S
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