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RePS: a sequence assembler that masks exact repeats identified from the shotgun data
Jun Wang1, Gane Ka-Shu Wong, Peixiang Ni
1Hangzhou Genomics Institute, Institute of Bioinformatics of Zhejiang University, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China. wangj@genomics.org.cn
Genome Research
|May 9, 2002
Summary
We developed RePS, a novel sequence assembler that removes repeats before assembly. This method enables accurate genome assembly even with low coverage and high repeat content.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genome assembly is challenging due to repetitive sequences.
- Existing assemblers struggle with high repeat content.
Purpose of the Study:
- To introduce RePS, a repeat-masked Phrap with scaffolding sequence assembler.
- To demonstrate effective genome assembly with low coverage and high repeat percentages.
Main Methods:
- RePS explicitly identifies and removes exact 20mer repeats from shotgun data.
- Error probabilities are computed for each base.
- Clone-end-pairing information is used for scaffolding to order and orient contigs.
Main Results:
- RePS achieves reasonable assemblies for human and rice genomes at 4x-6x coverage.
- The assembler effectively handles datasets with up to 42.2% exact repeats.
Conclusions:
- RePS provides a robust solution for genome assembly in the presence of significant repetitive elements.
- The software enables accurate base error probability calculation and contig scaffolding.