DMAP - Graphical representation of physical and genetic map correlation

Next-generation sequencing approaches coupled with appropriate assembly software can provide draft genome sequences of complex organisms as a series of unordered contigs in a timely and cost effective manner. Likewise, high throughput mapping technologies such as DArT and SNP platforms can provide a high density of sequence-anchored markers with which high resolution genetic maps can be constructed. Visualising and interpreting these data requires a new generation of tools as the volume of data leads to considerable redundancy and information overload in graphical representation. DMAP provides a highly configurable visual representation of physical and genetic map correlation, reducing data representation to an aesthetically acceptable degree. It also calculates an optimal orientation for the ordered sequence contigs, highlighting markers that are anomalous and contigs which may be in erroneous positions. Output is as PDF, allowing subsequent refinement prior to print publication and vector based representation for online supplementary figures. The perl scripts have few dependencies and code is freely available under a creative commons license (CC-BY) from the authors GitHub repository at http://github.com/davidmam/DMAP.git.