For better experience, turn on JavaScript!



Rainbow is a tool to cluster and assemble short reads sequences originating from restriction-site associated DNA sequencing (RAD-seq). The Rainbow algorithm discriminates repeats from heterozygous sequences by grouping the reads into haplotypes and creates a guide tree, and implements a greedy algorithm for contig assembly.


Sequence assembly


  • Operation: Sequence assembly; De-novo assembly
  • Input: FASTQ
  • Output: -
  • Software interface: Command-line user interface
  • Language: C
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: 2.0.4
  • Maturity: Beta
  • Credit: The National Nature Science Foundation of China
  • Contact: ruanjue _at_
  • Collection: -


Chong Z, Ruan J, Wu CI "Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads." Bioinformatics. 2012 Nov 1;28(21):2732-7. Epub 2012 Sep 1.
PMID: 22942077

Chen D, Eulenstein O, Fernández-Baca D "Rainbow: a toolbox for phylogenetic supertree construction and analysis." Bioinformatics
PMID: 15145807

Download and documentation

If you find errors, please report here.