Since its emergence almost 20 years ago (Schwartz et al., Science 1995), optical mapping data has undergone a transition from laboratory technique to commercially available data generation method. In line with this transition, it is only relatively recently that optical mapping has started to be used for scaffolding contigs and assembly validation and verification in several large-scale sequencing projects --- for example, the goat (Dong et al., Nature Biotech. 2013) and amborella (Chamala et al., Science 2013) genomes. One major hurdle to the wider use of optical mapping

One fundamental problem that persists in this analysis is the efficient alignment of in-silico digested contigs to an optical map. We develop Twin to tackle this very problem. Twin is the first index-based method for aligning in-silico digested contigs to an optical map. Our results demonstrate that Twin is orders of magnitude faster than competing methods on a range of genomes.

Most-importantly, it is specifically designed to be capable of dealing with very large eukaryote genomes and thus, is the only non-proprietary method capable of completing the alignment for the budgerigar genome in a reasonable amount of time. The genome assemblies, optical maps, and files detailing the reads and assembly process are available for download at Table 1 demonstrates the statistics on the assemblies generated using short read data and Table 2 illustrates the performance of Twin with respect to that of competing tools on the assemblies of these genomes and their accompanied optical map. ß

Funding was provided by the National Institutes of Health through the Colorado Clinical and Translational Sciences Institute (CCTSI).