bait: organizing genomes and mapping rearrangements in single cells

strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (sces) and otherrearrangements. to analyze these data, we introduce bait, software which assigns templates and identifies andlocalizes sces. we demonstrate bait can refine completed reference assemblies, identifying approximately 21 mb ofincorrectly oriented fragments and placing over half (2.6 mb) of the orphan fragments in mm10/grcm38. bait alsostratifies scaffold-stage assemblies, potentially accelerating the assembling and finishing of reference genomes. baitis available at http://sourceforge.net/projects/bait/.