RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer 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. The updated version of RePS incorporates some of the ideas introduced by Phusion on clustering
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Wang J, Wong GK, Ni P, etal.
RePS: a sequence assembler that masks exact repeats identified from the shotgun data.
Genome Res 2002; 12: 824-31.