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[ Kaynak: bio-rainbow  ]

Paket: bio-rainbow (2.0.4+dfsg-1)

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.

bio-rainbow ile İlgili Diğer Paketler

  • bağımlılıklar
  • tavsiye edilen
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  • dep: libc6 (>= 2.14) [amd64]
    GNU C Library: Shared libraries
    ayrıca şunun tarafından sağlanan bir sanal paket libc6-udeb
    dep: libc6 (>= 2.4) [armhf]
  • dep: perl
    Larry Wall's Practical Extraction and Report Language

bio-rainbow indir

Tüm mevcut mimariler için indir
Mimari Paket Boyutu Kurulu Boyut Dosyalar
amd64 50,7 kB161 kB [dosya listesi]
armhf 47,4 kB128 kB [dosya listesi]