Package: bio-rainbow (2.0.4+dfsg-2)

[ Source: bio-rainbow  ]

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.

Other Packages Related to bio-rainbow

• dep: libc6 (>= 2.29)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: perl

  Larry Wall's Practical Extraction and Report Language

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Architecture	Package Size	Installed Size	Files
i386	63.9 kB	203.0 kB	[list of files]