Package: bio-rainbow (2.0.4+dfsg-2)
Links for bio-rainbow
Debian Resources:
Download Source Package bio-rainbow:
- [bio-rainbow_2.0.4+dfsg-2.dsc]
- [bio-rainbow_2.0.4+dfsg.orig.tar.xz]
- [bio-rainbow_2.0.4+dfsg-2.debian.tar.xz]
Maintainers:
- Debian Med Packaging Team (QA Page, Mail Archive)
- Olivier Sallou (QA Page)
- Pranav Ballaney (QA Page)
External Resources:
- Homepage [sourceforge.net]
Similar packages:
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 bio-rainbow
Architecture | Package Size | Installed Size | Files |
---|---|---|---|
mips64el | 61.4 kB | 209.0 kB | [list of files] |