What should the next generation of sequencing software look like?

[cBell]

The biggest thing for me is that no matter how much "heaving lifting" the software does, there is always something that I want to do that it doesn't.  So the software I choose to use will keep all the data easily accessible.  While any file format can eventually be reverse engineered, using XML and plain text and documented formats allow me to easily write small programs to modify the data to my heart's content.

[tonyv2842]

I want to thank everybody for their input.  Given the responses I've gotten, I can say that I am formulating (what I believe) will meet most if not all of these goals.  I need to brainstorm some more and no doubt it will be months before I actually start sharing my thoughts about what it is I have in mind.  If anyone thinks there might be anything else they'd like to share, please do.

[ptone]

I want to thank everybody for their input.  Given the responses I've gotten, I can say that I am formulating (what I believe) will meet most if not all of these goals.  I need to brainstorm some more and no doubt it will be months before I actually start sharing my thoughts about what it is I have in mind.  If anyone thinks there might be anything else they'd like to share, please do.

I'm a bit perplexed by your tone throughout this thread.  

What exactly are you formulating?  A spec of some sort?  Are you a software developer who actually intends to follow through on whatever it is that you "have in mind"?  Do you plan on it being commercial or free?  OpenSource?

I would be interested in hearing more about what your objectives and goals are.  I *think* you are just wanting to help articulate what is needed by the community - but may I suggest such efforts are a collective process, not something to take on in isolation.  I've edited this post because after looking at your profile, I see you are recent to the scene (as am I) and have not had a CC show - so I'm now clearer that you are not a developer, but just interested in helping clarify needs and goals.  But I will tell you that given the amount of work in actually writing such software, the author will ultimately be more familiar with the details and practical challenges and opinionated with the approaches and tradeoffs they will take.  Such software is a LOT of work.

Look forward to seeing what you formulate.  Hopefully by then my software will already be out there for folks to try out.

-P

[tonyv2842]

ptone, I wanted to understand the problems people were facing and started the thread to get them out in the open in the hopes that everyone would benefit and think about the problems and their solutions.  I myself want to offer suggestions as well but only wish to do so once I fully understand the problem.  I agree with you in regards to the pride born of taking on such an endeavor.  I certainly wish you good luck with yours and would also like to hear your thoughts with regards to the solution.
Tony