Do a genome browser exists where you can easily import your own prokaryotic draft genomes (stacks of contigs) and add custom tracks such as NGS mapping data and RAST annotations? I would prefer a web based browser over a desktop based browser, but that totally depends on ease of use and functionality (especially importing custom genomes and tracks).
I find adding custom genomes to Gbrowse painful. Jbrowse is not mature and development has unfortunately stalled. The UCSC Genome browser and Ensembl are not meant for prokaryotes - same for IGV and GenPlay. Artemis don't work well with draft genomes unless you create a single sequence scaffold.
FYI JBrowse is a mature genome browser and is now actively developed - seehttp://jbrowse.org for information.
I am following JBrowse closely. It is maturing nicely, but still misses the options to setup new genomes and tracks easily.
Are you on the JBrowse mailing list ( http://jbrowse.org/contact/ )? I suggest that you give your feedback to Rob Buels, the developer; he's extremely receptive to comments and suggestions, and it's the best way to ensure that your concerns get addressed.
I know. I have corresponded a bit with Rob.