WARNING: This is alpha software. If it breaks free of your server and goes on a murderous rampage through your FASTQ files, don't blame me.
Use features of the Genotyping-by-Sequencing protocol to intelligently remove second-read read-though from GBS data.
This removes adaptor contamination, as well as removing the second read of a read-through pair, so that the number of reads per locus/allele is not inflated.
More to come, this is just the initial blurb.