Documentation on how to install and run our Java pipeline for GBS Bioinformatics is available here
The java source code can be downloaded from the TASSEL page on SourceForge. The GBS pipeline code is under the classpath net.maizegenetics.gbs.pipeline. Instructions on how to check out this source code into NetBeans are available here.
UNEAK is the non-reference-genome GBS pipepline in TASSEL. UNEAK documentation is here.
Workshops on GBS Bioinformatics are offered at Cornell University on a regular basis. More information on GBS Bioinformatics workshops can be found here.
Videos from the workshop held in February 2012 are available here.