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

[ 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) [not alpha, ia64, riscv64, sh4]

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

  dep: libc6 (>= 2.31) [sh4]

  dep: libc6 (>= 2.34) [riscv64]

• dep: libc6.1 (>= 2.29) [alpha]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

  dep: libc6.1 (>= 2.31) [ia64]

• dep: perl

  Larry Wall's Practical Extraction and Report Language

Download bio-rainbow

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	2.0.4+dfsg-2	62.7 kB	210.0 kB	[list of files]
amd64	2.0.4+dfsg-2	58.8 kB	186.0 kB	[list of files]
arm64	2.0.4+dfsg-2	58.1 kB	178.0 kB	[list of files]
armel	2.0.4+dfsg-2	56.7 kB	179.0 kB	[list of files]
armhf	2.0.4+dfsg-2	56.0 kB	143.0 kB	[list of files]
hppa (unofficial port)	2.0.4+dfsg-2	63.2 kB	194.0 kB	[list of files]
i386	2.0.4+dfsg-2	63.9 kB	203.0 kB	[list of files]
ia64 (unofficial port)	2.0.4+dfsg-2	75.4 kB	311.0 kB	[list of files]
m68k (unofficial port)	2.0.4+dfsg-2	56.1 kB	175.0 kB	[list of files]
mips64el	2.0.4+dfsg-2	61.4 kB	209.0 kB	[list of files]
ppc64 (unofficial port)	2.0.4+dfsg-2	65.8 kB	306.0 kB	[list of files]
ppc64el	2.0.4+dfsg-2	65.6 kB	306.0 kB	[list of files]
riscv64	2.0.4+dfsg-2+b2	63.0 kB	163.0 kB	[list of files]
s390x	2.0.4+dfsg-2	55.9 kB	194.0 kB	[list of files]
sh4 (unofficial port)	2.0.4+dfsg-2	65.9 kB	167.0 kB	[list of files]
sparc64 (unofficial port)	2.0.4+dfsg-2	52.9 kB	181.0 kB	[list of files]
x32 (unofficial port)	2.0.4+dfsg-2	59.3 kB	183.0 kB	[list of files]