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.
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. https://doi.org/10.1073/pnas.1220349110
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