I recently created a repository on GitHub for an application that I wrote a year and a half ago to generate fragment recruitment plots; it is located at https://github.com/mstrosaker/fragrecruit . These plots are used in genomic and metagenomic analysis to visualize how short reads align to one or more reference genomes. The application is written in Python, using matplotlib to generate the plots.
One such plot is shown below. This plot shows the reads from human keratinized gingiva microbiome samples that align against a 100000bp section of the genome of a strain of the bacteria Gemella haemolysans. Each sample is represented by a different color. The sample sizes are dramatically different (reflecting differing depth of sequencing among the samples), which makes some colors much more predominant. My application adds vertical lines to delineate the boundaries of contigs in the reference genome, and shades alternate contigs; as far as I know, it is the only application that identifies contigs along the reference genome in this manner. It is interesting to note that, in some cases, fragments may tend to cluster near the edges of contigs; I suspect this is often due to the presence of repetitive sequences at the ends of contigs.