This repository contains a number of bash and R scripts used in the processing of RADSeq data on the VSC supercomputer.
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Updated
Apr 6, 2022 - Shell
This repository contains a number of bash and R scripts used in the processing of RADSeq data on the VSC supercomputer.
Assembly, analysis and visualization of ddRAD seq data for the plant genus Muscari.
R script employed in the manuscript 'Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii' to compute the distribution of FIS across loci into discrete classes
grur: an R package tailored for RADseq data imputations
R script employed in the manuscript 'Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii' to compute the frequency of pairwise genetic distances among individuals.
Set of scripts to process RAD-Seq HTS data on computing grids like MetaCentrum.
pipeline for optimizing the clustering threshold in ipyrad RADseq assemblies
Analyse RAD-tags and generate the Genetic Map with GWAS
Electronic notebook for "Deep reefs are not universal refuges: reseeding potential varies among coral species" (Science Advances, 2017)
Genomics pipeline to reproduce the analysis from Matthey-Doret et al., 2019, Genome Biology and Evolution
GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.
Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)
Random scripts, mostly for dealing with RADseq data and DNA sequence alignments
Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.
Population assignment analysis using R
Simple program for in silico restriction digest of genomic sequences, to simulate RAD-family NGS library prep methods
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