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RACA is a tool to order and orientate scaffolds generated from short-read based scaffolds using reference genomes from closely related species. The tool takes advantage of conservation of homologous sequences and has demonstrated good performance in simulated and real datasets. The tool is suitable for assemblies made from short reads and no linkage map is available.


Sequence assembly


  • Operation: Scaffolding; Reference-based scaffolding
  • Software interface: Command-line user interface
  • Language: -
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: National Science Foundation; National Institutes of Health/National Human Genome Research Institute
  • Contact: jianma _at_
  • Collection: -


Kim J, Larkin DM, Cai Q, Asan, Zhang Y, Ge RL, Auvil L, Capitanu B, Zhang G, Lewin HA, Ma J "Reference-assisted chromosome assembly." Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1785-90. 10.1073/pnas.1220349110. Epub 2013 Jan 10.
PMID: 23307812
PMCID: PMC3562798

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