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repdenovo website  

REPdenovo is designed for constructing repeats directly from sequence reads. It based on the idea of frequent k-mer assembly. REPdenovo provides many functionalities, and can generate much longer repeats than existing tools. The overall pipeline is shown in the mannual file. REPdenovo supports the following main functionalities.

Required Modules


  • gcc/5.2.0
  • repdenovo

System Variables

  • HPC_REPDENOVO_DIR - installation directory
  • HPC_REPDENOVO_BIN - executable directory
  • HPC_REPDENOVO_DOC - documentation directory
  • HPC_REPDENOVO_EXE - sample directory


If you publish research that uses repdenovo you have to cite it as follows:

Chong Chu, Rasmus Nielsen and Yufeng Wu, REPdenovo: Inferring de novo repeat motifs from short sequence reads, PLoS One 11.3 (2016): e0150719.