ASSIsT: the automated SNP scoring Tool

ASSIsT is a tool for the efficient filtering of Illumina Infinium/BeadExpress based SNP markers. It allows analysis of different type of experimental population, namely Cross Pollinated (CP - F1), Back Cross (BC), F2 and collections of unrelated individuals (Germplasm).
Results can be exported to different formats and therefore can be fed straight to marker-trait association analysis software like FlexQTL, HapMap, GAPIT, JoinMap, PLINK, Structure and Tassel.

Downloads
A pdf version of the user manual can be found here.
The Windows installation package can be found here.
The Source Code can be found here.
Sample data files can be found here.