Pacote: bio-rainbow (2.0.4+dfsg-2 e outros)

[ Fonte: 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.

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Download de bio-rainbow

Baixe para todas as arquiteturas disponíveis

Arquitetura	Versão	Tamanho do pacote	Tamanho instalado	Arquivos
amd64	2.0.4+dfsg-2	58.8 kB	186.0 kB	[lista de arquivos]
arm64	2.0.4+dfsg-2+b2	58.3 kB	307.0 kB	[lista de arquivos]
armel	2.0.4+dfsg-2	56.7 kB	179.0 kB	[lista de arquivos]
armhf	2.0.4+dfsg-2	56.0 kB	143.0 kB	[lista de arquivos]
i386	2.0.4+dfsg-2	63.9 kB	203.0 kB	[lista de arquivos]
mips64el	2.0.4+dfsg-2	61.4 kB	209.0 kB	[lista de arquivos]
ppc64el	2.0.4+dfsg-2	65.6 kB	306.0 kB	[lista de arquivos]
riscv64	2.0.4+dfsg-2+b3	63.3 kB	163.0 kB	[lista de arquivos]
s390x	2.0.4+dfsg-2	55.9 kB	194.0 kB	[lista de arquivos]