Tag: RADseq

RADinitio 1.1.1 – Simulation software for the Selection and Optimization of RADseq Experiments

RADinitio 1.1.1

:: DESCRIPTION

RADinitio is a forward simulator for creating population-level RAD data sets, based on a given reference genome. This in silico RADseq library preparation and sequencing process, allows for the exploration of parameters including restriction enzyme selection, library insert size, PCR duplicate distribution, and sequencing coverage.

DEVELOPER

Cresko labs

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RADinitio

:: MORE INFORMATION

Citation:

Rivera-Colón AG, Rochette NC, Catchen JM.
Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data.
Mol Ecol Resour. 2021 Feb;21(2):363-378. doi: 10.1111/1755-0998.13163. Epub 2020 May 20. PMID: 32275349.

PyRAD 3.0.66 – Assembly of de novo RADseq loci for Phylogenetic Analyses

PyRAD 3.0.66

:: DESCRIPTION

PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 PyRAD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 20.
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses.
Eaton DA.