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

[ Källkod: 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.

Andra paket besläktade med bio-rainbow

• dep: libc6 (>= 2.29)

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6-udeb

• dep: perl

  Larry Wall's Practical Extraction and Report Language

Hämta bio-rainbow

Hämtningar för alla tillgängliga arkitekturer

Arkitektur	Paketstorlek	Installerad storlek	Filer
amd64	58,8 kbyte	186,0 kbyte	[filförteckning]
arm64	58,1 kbyte	178,0 kbyte	[filförteckning]
armel	56,7 kbyte	179,0 kbyte	[filförteckning]
armhf	56,0 kbyte	143,0 kbyte	[filförteckning]
i386	63,9 kbyte	203,0 kbyte	[filförteckning]
mips64el	61,4 kbyte	209,0 kbyte	[filförteckning]
mipsel	59,9 kbyte	202,0 kbyte	[filförteckning]
ppc64el	65,6 kbyte	306,0 kbyte	[filförteckning]
s390x	55,9 kbyte	194,0 kbyte	[filförteckning]