Lex Nederbragt has written a post outlining his thoughts on what any Assemblathon 3 contest should look like. This is something that Ian Korf will be talking about today at the Genome 10K meeting which is happening at the moment (though it seems that there has been a lot of discussion about this in other sessions). From his post:

I believe it is here the Assemblathon 3 could make a contribution. By switching the focus from the assembly developers to the assembly users, Assemblathon 3 could help to answer the question:

How to choose the ‘right’ assembly from a set of generated assemblies