I have been a professional software developer since 1998 after I got my masters degree in computer science. Yet, when I try to do some simple next-gen analysis, there are so many software tools with different flavors which require different input file formats, different options, with different pros and cons, and most of which are poorly documented. It's really a pain in the ass and a shame for me not being able to just "hookup" (pipelining) such programs together.
My question is: do we have a better solution? Say, one stop shop for NGS analysis? If not, who is interested in building up such a shop? Maybe we can figure out a better way to do NGS for everyone.