Agreed, you will need to install a Linux OS in order to effectively deal with NGS sequence data. I recommend dual-booting Linux (I use Ubuntu) and Windows by partitioning your hard drive, as this should be better performance-wise than using a thumb drive. There are tutorials all over the internet, such as this one (hasn't been vetted): http://www.linuxandubuntu.com/home/dual-boot-ubuntu-15-04-14-10-and-windows-10-8-1-8-step-by-step-tutorial-with-screenshots
That being said, I think Bowtie (http://bowtie-bio.sourceforge.net/tutorial.shtml) is one short-read assembler which works on Windows, but I have never tried it myself.