Codes i wrote for the paper "genomic resources for Mediterranean fishes"

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 frequency of pairwise genetic distances among individuals.

Set of scripts to process RAD-Seq HTS data on computing grids like MetaCentrum.

Random scripts for dealing with ddRAD data, including output from pyRAD

This repository contains a number of bash and R scripts used in the processing of RADSeq data on the VSC supercomputer.

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

Populations genomics in R, Workshop in Hobart, Tasmania

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

pipeline for optimizing the clustering threshold in ipyrad RADseq assemblies

GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.

Analyse RAD-tags and generate the Genetic Map with GWAS

Simple program for in silico restriction digest of genomic sequences, to simulate RAD-family NGS library prep methods

grur: an R package tailored for RADseq data imputations

Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)

Detects and blacklists paralog RAD loci analyzed in Stacks or ipyrad, based on the McKinney 2017 method (doi:10.1111/1755-0998.12613)

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

Random scripts, mostly for dealing with RADseq data and DNA sequence alignments