There's a great new paper in bioRxiv by Alejandro Hernandez Wences and Michael Schatz. They directly address something I wondered about as we were running the Assemblathon contests. Namely, can you combine some of the submitted assemblies to make an even better assembly? Well the answer seems to be a resounding 'yes'.

For each of three species in the Assemblathon 2 project we applied our algorithm to the top 6 assemblies as ranked by the cumulative Z-score reported in the paper…

We evaluated the correctness and contiguity of the metassembly at each merging step using the metrics used by the Assemblathon 2 evaluation…

In all three species, the contiguity statistics are significantly improved by our metassembly algorithm

Hopefully their Metassembler tool will be useful in improving many other poor quality assemblies that are out there!