“Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype-calling accuracy” paper published!

Together with our collaborators from the National University of Singapore we just published a paper describing an improved method for making double-digest RAD-tag libraries. By adding a small run of degenerate nucleotides to the end of one of the Illumina indexes, you can barcode each individual ligation reaction and determine how many molecules participate in each reaction. This is a simple modification, that allows us to confidently make RAD-tag libraries using just a few nanograms of input material. The actual library preparation is not different — in this paper we describe a protocol that we use to process thousands of samples using a liquid handling robot, making 96 libraries at once.