multiplexed shotgun genotyping
We followed the protocol of Andolfatto et al, Genome Research 2011: Multiplexed Shotgun Genotyping.  Genomic DNA of 96 individuals is digested with MseI, and one of 96 unique barcoded flow cell linkers is ligated onto digested genomic DNA. The purified 250-300bp library is amplified with standard FC primers. For sequencing, a custom foreshortened flow cell primer is used: 5'-ACACTCTTTCCCTACACGACGCTCTT CCGA-3' More specific details for the protocol may be found at Cande et al, PLoS ONE, 2012, or in Erezyilmaz and Stern upon publication.