ezmsim
clustering and assembling short reads for bioinformatics
Install
- All systems
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curl cmd.cat/ezmsim.sh
- Debian
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apt-get install bio-rainbow - Ubuntu
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apt-get install bio-rainbow - Kali Linux
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apt-get install bio-rainbow - Windows (WSL2)
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sudo apt-get updatesudo apt-get install bio-rainbow - Raspbian
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apt-get install bio-rainbow - Dockerfile
- dockerfile.run/ezmsim
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.