I took the newly created course (given first time this spring) "Genome Bioinformatics" at Uppsala University, to get some grounding for my work at UPPMAX HPC center to support UPPNEX users with NGS analysis. (I had some bioinformatics background, but not specifically in NGS).
The course is heavily focused on NGS analysis, and quickly gave me good insight into the typical NGS analysis workflow, probably much because the course plan revolved around hands-on computer labs, where we got to do all the typical things like alignment, assembly, extract info from fastq files etc , while the lectures served to support the hands-on labs with the relevant background theory.
I can highly recommend the course for anyone new to NGS analysis, who is able to spend some four weeks in Uppsala. (Yes, the course is given in English).
 Using the typical tools such as samtools, bwa, awk etc, in a linux environment. I also heard from the course organizers that they plan for next year to allow doing the computations at UPPMAX, which will give course participants the added benefit of some HPC experience.