Stacks 2.59 – Analyse RAD Sequencing data

Stacks 2.59

:: DESCRIPTION

Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.

DEVELOPER

Cresko labs

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX
MySQL
Perl
MDB2 Pear Module

:: DOWNLOAD

Stacks

:: MORE INFORMATION

Citation:

J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait.
Stacks: building and genotyping loci de novo from short-read sequences.
G3: Genes, Genomes, Genetics, 1:171-182, 2011

simRRLs 1.5 – Simulate fastQ formatted RAD, ddRAD or GBS data on a fixed Species Tree

simRRLs 1.5

:: DESCRIPTION

The script simRRLs.py can be used to simulate RADseq-like sequences on a fixed species tree under a coalescent model. See Example usage page for advanced options, including simulating missing data, indels and different levels of divergence between taxa.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows
Python

:: DOWNLOAD

simRRLs

:: MORE INFORMATION

Rainbow v2.0.4 – Clustering and Assembling Short Reads, especially for RAD

Rainbow v2.0.4

:: DESCRIPTION

Rainbow package consists of several programs used for RAD-seq related clustering and de novo assembly.

::DEVELOPER

Rainbow team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

Rainbow

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 1;28(21):2732-7. doi: 10.1093/bioinformatics/bts482.
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads.
Chong Z, Ruan J, Wu CI.