Pakket: bio-rainbow (2.0.4+dfsg-2 en anderen)

[ Bron: 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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bio-rainbow downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Versie	Pakketgrootte	Geïnstalleerde grootte	Bestanden
amd64	2.0.4+dfsg-2	58,8 kB	186,0 kB	[overzicht]
arm64	2.0.4+dfsg-2+b1	58,1 kB	307,0 kB	[overzicht]
armel	2.0.4+dfsg-2	56,7 kB	179,0 kB	[overzicht]
armhf	2.0.4+dfsg-2	56,0 kB	143,0 kB	[overzicht]
i386	2.0.4+dfsg-2	63,9 kB	203,0 kB	[overzicht]
mips64el	2.0.4+dfsg-2	61,4 kB	209,0 kB	[overzicht]
ppc64el	2.0.4+dfsg-2	65,6 kB	306,0 kB	[overzicht]
riscv64	2.0.4+dfsg-2+b2	63,0 kB	163,0 kB	[overzicht]
s390x	2.0.4+dfsg-2	55,9 kB	194,0 kB	[overzicht]