radseq

RADseq Data Exploration, Manipulation and Visualization using R

Collection of Python scripts for parsing/analyses of RAD-seq data

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

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

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

grur: an R package tailored for RADseq data imputations

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

Analyse RAD-tags and generate the Genetic Map with GWAS

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

Genomics pipeline to reproduce the analysis from Matthey-Doret et al., 2019, Genome Biology and Evolution

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

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

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

Electronic notebook for "Deep reefs are not universal refuges: reseeding potential varies among coral species" (Science Advances, 2017)

This repository provides a comprehensive tutorial for phylogenetic analysis, covering data collection, sequence alignment, tree construction, and interpretation. It runs on AWS SageMaker using Jupyter notebooks and includes tools like MAFFT, Nextclade, and IQ-TREE.

pipeline for optimizing the clustering threshold in ipyrad RADseq assemblies

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

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