We have recently done a lot of work on adapting MEGAN so as to support the analysis of long reads and contigs. We refer to this major extension of MEGAN as MEGAN-LR.
We presented this work at CAMDA in Prague earlier this year and a manuscript describing it is currently under review. The manuscript is available on BioRxiv: MEGAN-LR: New algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs