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Repository smudgeplot
Name: smudgeplot
Owner: galaxy-australia
Synopsis: Inference of ploidy and heterozygosity structure using whole genome sequencing
This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc. Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs.
Content homepage: https://github.com/KamilSJaron/smudgeplot
Development repository: https://github.com/galaxyproject/tools-iuc
Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/galaxy-australia/smudgeplot/5e0825476fb7
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot
Type: unrestricted
Revision: 4:5e0825476fb7
This revision can be installed: True
Times cloned / installed: 318

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Name Description Version Minimum Galaxy Version
inference of ploidy and heterozygosity structure using whole genome sequencing 0.2.5+galaxy+2 21.05

Categories
Assembly - Tools for working with assemblies