bio-rainbow - 2.0.4+dfsg-2 main

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.