<![CDATA[BOL: Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads]]> https://bioinformaticsonline.com/bookmarks/view/37959/rainbow-an-integrated-tool-for-efficient-clustering-and-assembling-rad-seq-reads? https://bioinformaticsonline.com/bookmarks/view/37959/rainbow-an-integrated-tool-for-efficient-clustering-and-assembling-rad-seq-reads Fri, 19 Oct 2018 08:23:42 -0500 https://bioinformaticsonline.com/bookmarks/view/37959/rainbow-an-integrated-tool-for-efficient-clustering-and-assembling-rad-seq-reads <![CDATA[Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads]]> 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. And along 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, we show that Rainbow is more competent than the other tools in dealing with RAD-seq data

Address of the bookmark: https://sourceforge.net/projects/bio-rainbow/files/

]]> Rahul Nayak