A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data.  This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations.

Associated manuscript:

Andolfatto P., Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL. 2011. Multiplexed Shotgun Genotyping for Rapid and Efficient Genetic Mapping.  Genome Research, 21(4):610-7. [PubMed].

Downloads: https://github.com/JaneliaSciComp/msg

An example: https://github.com/JaneliaSciComp/msg/tree/master/example

Instructions: https://github.com/JaneliaSciComp/msg/tree/master/instructions

README: https://github.com/JaneliaSciComp/msg/blob/master/README