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

[ Quellcode: 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.

Andere Pakete mit Bezug zu bio-rainbow

• dep: libc6 (>= 2.29)

  GNU-C-Bibliothek: Laufzeitbibliotheken
  auch ein virtuelles Paket, bereitgestellt durch libc6-udeb

• dep: perl

  Larry Wall's Practical Extraction und Report Language

bio-rainbow herunterladen

Download für alle verfügbaren Architekturen

Architektur	Paketgröße	Größe (installiert)	Dateien
i386	63,9 kB	203,0 kB	[Liste der Dateien]