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Vol. 12, Issue 5, 824-831, May 2002

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

Jun Wang,1,2,3,5 Gane Ka-Shu Wong,1,2,4,5 Peixiang Ni,2 Yujun Han,2 Xiangang Huang,2 Jianguo Zhang,2 Chen Ye,2 Yong Zhang,2,3 Jianfei Hu,2,3 Kunlin Zhang,2,3 Xin Xu,1 Lijuan Cong,1 Hong Lu,1 Xide Ren,1 Xiaoyu Ren,1 Jun He,1 Lin Tao,1,2 Douglas A. Passey,4 Jian Wang,1,2 Huanming Yang,1,2 Jun Yu,1,2,4 and Songgang Li2,3

1 Hangzhou Genomics Institute, Institute of Bioinformatics of Zhejiang University, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China; 2 Beijing Genomic Institute, Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing, 101300, China; 3 College of Life Sciences, Peking University, Beijing, 100871, China; 4 University of Washington Genome Center, Department of Medicine, Fluke Hall, M/C 352145, Seattle, Washington 98195, USA

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[The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: P. Green and A.F. Smit.]

5 Corresponding authors.

12:824-831 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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