Source: bio-rainbow Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Section: science Priority: optional Build-Depends: debhelper (>= 11~), help2man Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/med-team/bio-rainbow Vcs-Git: https://salsa.debian.org/med-team/bio-rainbow.git Homepage: http://sourceforge.net/projects/bio-rainbow/ Package: bio-rainbow Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends} Description: clustering and assembling short reads for bioinformatics Efficient tool for clustering and assembling short reads, especially for RAD. . Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top-down manner. long a guided tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, it is shown that Rainbow is more competent than the other tools in dealing with RAD-seq data.