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RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data

2002; Cold Spring Harbor Laboratory Press; Volume: 12; Issue: 5 Linguagem: Inglês

10.1101/gr.165102

1549-5469

Jun Wang, Gane Ka‐Shu Wong, Peixiang Ni, Yujun Han, Xiangang Huang, Jianguo Zhang, Chen Ye, Yong Zhang, Jianfei Hu, Kunlin Zhang, Xin Xu, Lijuan Cong, Hong Lü, Xide Ren, Xiaoyu Ren, Jun He, Lin Tao, Douglas A. Passey, Jian Wang, Huanming Yang, Jun Yu, Songgang Li,

Chromosomal and Genetic Variations

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 [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: P. Green and A.F. Smit.]