For those 92.2% desktop users out there: http://en.wikipedia.org/wiki/Usageshareofoperatingsystems
BOW http://bow.codeplex.com/ is my little effort to help you to use your everyday computer on Bioinfo/sequencing.
Current list of programs: (natively run on Windows x64)
2, BWA with multithreaded SAMPE
In the making:
5, SamCompare (a WPF GUI program enable you to compare two SAM/BAM files single/paired end, line by line, tag by tag, to 'debug' your alignment running (i.e. to understand which parameter does what; or to tell if a fancy re-aligner really is that good, just give an example of possible usage.))
6, SequencingStudio (a WPF GUI program enable you to open all kinds of text/binary files, view with visualization, convert, align, call variant, offload work to the cloud, etc.)
Beta testing: Windows Azure (The Microsoft Cloud) pipleline, I recently did a demo at the Microsoft eScience 2012 workshop of the running system. http://research.microsoft.com/en-US/events/escience2012/agenda.aspx, (DemoFest, 12,000 Human Genomes from Raw Sequence to Result, on Windows and Windows Azure ).
The system is built like a Sun Grid Engine or HPC Cluster in that sense is not limited to process seqence files only. You as a user only need to upload your files to a container, and grab a Recipe (job flow), final results can be in files or databases. The beauty of Cloud is the Utility Model, i.e. you purchase your computing hours like water and electricity, no upfront investment of a local cluster, zero maintenance, zero IT budget/salary. Just a credit card (Purchase Order is accepted too), you can have your own 1000 core cluster up and running in no time, and delete it when your job done.
It might somehow sounds like Galaxy or BaseSpace, in that 1, I don't know much deep about those systems, 2, my team size is one.
If you are interested to try out, please contact me. Or you have any suggestions, comments, bricks, programs you want on Windows, etc., just let me know.
p.s. If you like this thread, maybe kindly ask moderators to pin this on top.