ezmsim

clustering and assembling short reads for bioinformatics

Install

All systems
curl cmd.cat/ezmsim.sh
Debian Debian
apt-get install bio-rainbow
Ubuntu
apt-get install bio-rainbow
image/svg+xml Kali Linux
apt-get install bio-rainbow
Windows (WSL2)
sudo apt-get update sudo apt-get install bio-rainbow
Raspbian
apt-get install bio-rainbow

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.